Battery charging questions Parallel charging and battery balancing of LiPos
What colour is the magic smoke when it vents with flame ? :-)

Rushing immensely, more later,  but ...

What you describe seems to run a severe risk of doing damage.

To be ure, first you need to specify the allowed MAX charge rate for each LiPo.   

You have 1.0 + 1.2 = 2.2 Ah in parallel so 5A = 5/2.2 = 2.27C.
 This MAY be OK if cells are specd as 2C or more and are balanced in draw.
 If specd at say 10C then it all may survive.
 If specd at 1C it is very very bad.  

BUT when a cell pair plateaus at 8.4V it's current will start to drop and if the charger is able to make 5A the extra current WILL flow into the still in current more other battery pair. 

If max charge rates are not >> 2C then what you describe is at best an extremely poor compromise and at worst a disaster either in magic smoking or in cell lifetimes. 

If max charge rates are around 2C then what you describe is at best a beating of some of the cells regularly and at worst a journey towards magic smokedom.



In an arrangement like this with different capacity pairs wired in parallel you need to carefully monitor individual cell pair or even cell voltages to prevent discharge-damage. This is going to make balancing more important, although I have been impressed with how well cells from the same batch seem to track when I have checked it (not often).

Operating cells of different capacities in parallel is an immednsely bad idea usually unless you manage and turn off each pair individually.

Apart from one pair endpointing before the other and throwing more charge or discharge onto the other there is a lack of certainty re how cells load share.
 eg Say you have a 1000 and 1200 mAh cell and load both with 1000 mA. The large cell will see this as less of a percentage load so it's natural terminal voltage will be larger and it will "happily" supply the extra current. but there is no guarantee that it will o this in the ratio of the tywo capacities. The large cell may prove very "sacrificial and provide most of the load for most of its capacity. BUT when it finally falters the small cell will then take up most of the load and may now be overloaded. And there is no certainty that the LARGE cells will not now expire and be driven into a damaging mode. Probably not, but. too many uncertainties. 

Why run cells of different sizes and in this 2 x 2 pattern?



Key question: What are the max allowable charge current rates for the 1000 and 1200 mAh cells.
 Without this information the question become svery hard to give a good answer to.