Electron transfer and thermal efficiency in series vs single battery?
If you have 10 batteries in series all generating 5W, does every battery in the series have the same temperature as a single battery drawing 5W? I have trouble visualizing how the electrons travel from the middle batteries. Does the transfer make the series version run hotter?


The question can be answered without reference to the labours of electrons.
Occam opines that if you can leave stuff out of your ponderings and still get an equally good answer, then it's preferable to do so. So ...

If you place 10 cells in series and each cell provides 5W of power then the output is 5w x 10 = 50 W.   Each cell of the overall battery sees conditions no different to what it would see if it was working by itself. Each cell passes the same current and each cell raises the potential of its positive pole by Vcell relative to its negative pole. A cell does not "know" what it's voltage is relative to some arbitrary remote point - such as the bottom of the battery stack or the top of the battery stack or the far side of the Moon. There may be some defined relationship (as there is in the 1st two examples above) but they do not affect what the individual cell does or "sees". Nor its electrons.

A water analogy should help.

THE FOLLOWING IS A "GOOD ENOUGH" BATTERY ANALOGY: 
Imagine having 10 pumps. Each can pump to a head of 1.5 metres at a flow rate of 1 litre per second. If a pump is "at pressure" and no flow occurs it idles at that pressure. If flow is required - as detected by any flow occurring it will instantaneously meet that flow demand at the rated head up to the maximum rated flow. 

Arrange the pumps in "series" - the first pump P1 draws from a pond and feeds the input of the next pump P2.
P2 feeds P3.
P3 .... 
P10 feeds an output valve.

If the output valve is closed all pumps will produce 1.5m head pressure at vtheir outputs relative to their input.
Of the input 'pond' is at level = 0 the P1 out head = 1.5m of head.

P2 in = 1.5 m of head.
It adds 1.5m of head so P2 out = 3m of head.  

This continues all the way up the "stack" so P10 out = 15m of head - still with no flow.

If the output valve is now opened to allow 0.5 l / second  of flow, the head pressure at each cell output will not change and the output will be 0.5 l/s at 15m of head pressure. If output demand exceeds 1 l/s knowledge outside the specification is needed to know what happens.

Note that in this case the illusion of isolation of each pump IS an illusion.
The top pump "sees 13.5m input pressure and adds 1.5 m to produce output at 15m head pressure. BUT the pump housing and seals ARE subject to a pressure of 15m of head at the outlet. If the pump housing is not strong enough the 15m of head pressure MAY rupture the housing and cause destruction of the pumping chain. This also applies to cells in a battery BUT is a condition seldom experienced.
If we stack 100,000 1 volt cells in series the top cell output is at 100,000 V relative to input. If we ground the input all is well enoughish as long as the breakdown voltage of anything between high voltage and ground is large enough. But if we eg stand on ground and bring a cautious finger near to the casing of a cell near the top of the stack we will reach a point where we find we have not been cautious enough - electrons will cry 'freedom' and bad stuff will happen. BUT this is a consequence only if we expose the middle cells to conditions that break down their relative "isolation". 

Wrap up: In normal &amp; designed operation each cell in a series string in a battery acts as if it is in isolation. As long as there is no thermal coupling between cells then there are no intercell interactions. (Real batteries will have some degree of thermal coupling between cells in the same outer, but that's not the issue that you are seeking to address here).

Added:


  Can you give me some resources into thermal coupling for batteries? just so that I know the theory, for the moment I just think that thermal coupling is a magnetic change from different metals when they change temperature?


I'll copy the summary here as it covers the main point.


Very very roughly - the inside of a battery will be somewhat hotter than the outer surface temperature of the cells BUT the main factor is how well you take heat away from (= cool) either the battery or the bare cells. 


"Thermal coupling" in this context is "just" the sharing of heat between cells so that they become hotter that they would have been if isolated. No magnetics involved. 

The 3 modes of heat transfer are radiation, convection and conduction. In a battery pack there are individual cells in close proximity with some air around them and a "shell". It's not too important what mode of transfer is used but in a LiPo pack conduction would be a major factor whereas with cylindrical cells convection and radiation would play larger roles.   

With LiPo batteries the calls are usually rectangular and flat, in contact and wrapped in a plastic outer. In batteries made from eg 18650 cylindrical cells they are close-packed, with insulating outers around the cells (usually plastic) and an outer case which may be rigid or a wrap. Usually at least semi rigid for more than a few cells. The thermodynamics of energy transfer out of the packs will be very much situation dependent but in LiPo flat batteries you can expect the middle "sandwiched" cells to be at a disadvantage for heat transfer. In a cyclindrical array I'd GUESSTIMATE that you could largely take the total thermal output in Watts and look at the outer area and it's thermal resistance and arrive at the temperature rise of the pack above open air cell temperatures. Term  resistance R is in degree C. Metre^2 per watt . Thickness matters but it  gets dealt with in the calculations.  Temperature rise T for thickness of outer in metres t, is   T =  W x R x t /A. BUT this doesn't help much as that is "just" the drop across the housing - it shows how much hotter the inside will be compared with the surface of the outer, but how you take heat away from the outer makes an immense difference. Very very roughly - the inside of a battery will be somewhat hotter than the outer surface temperature of the cells BUT the main factor is how well you take heat away from (= cool) either the battery or the bare cells. 

___________________________________

References:

Masters thesis - intro page
Design and Simulation of Passive Thermal Management System for Lithium-ion Battery Packs on an Unmanned Ground Vehicle

Thesis proper -122 pages

Battery University: 

Starter batteries.Some relevance.

BU-806a: How Heat and Loading affect Battery Life

BU-304a: Safety Concerns with Li-ion

Quora (caveat emptor) Does a LION battery heat up more during charge or discharge?

Legion