Shop Wiring Bewilderment
Return everything you can.
Go to the library and look at their books which are primers on doing home electrical wiring.  Browse all of their such books, and grab the one that seems in scope and feels the most accessible to you.  Read it thoroughly, not "twittery ADD skimming".   You can skip stuff like subpanels, wells, stoves and hot tubs since you're not doing that.  
Inventory what you still have.  
Think about what you want to do, and come back here and ask "here's what I want, here's what I've got, what advice do you have for minimal waste of material and keeping new purchases sane? 
Diagram out what you intend to do.  
Decide whether you are going cables vs conduit. 
Go to the town hall and pull a permit.   This will mean your plan gets some oversight from the local inspector, which will further help avert errors.  It will mean a final inspection/sign-off before completion.  It will also assure you don't get nailed on it when you sell your house and be forced to pay a pro to fix it out of your house proceeds. 
From now on, go to a genuine electrical supply house, rap with the clerk about how you are sick of big-box bad advice, but were there for the discounted prices, and that you had heard the were actually fairly priced.   The reason to do this is a) save money, and b) stop being poisoned by the absolutely awful advice dispensed by the $9/hour big-box clerks.  




Let's say we're at #4. 

Your proposal, as stated, will place 2 different circuits inside the same electrical box.  That's not a big deal, but it absolutely requires you understand keeping hots and neutrals separate.  It will also save wire to do this other ways. 

A separate circuit just for lights is very wise, but will be more expensive to wire.  

Putting your entire shop on one circuit is more concerning.  Depends what you plan to do with your shop. I just have to think you'd be better off with more than one circuit for receptacles if you can swing it.  One area it helps you is shop receptacles generally must be GFCI - lighting does not.  (Though if the main panel is above the flood zone and the circuit is not , GFCI always helps.) 

As a cost savings, I might make 1 circuit per section, putting the lighting on the receptacle circuit.  This avoids having 2 circuits in a box.  You run the risk of a breaker trip blacking out the lights, but you'll probably have at least 2 banks of lights on.  

When a freezer loses power, that's bad news, because usually nothing warns you of this.   Your worst risk is of a freezer in the same GFCI zone of a circuit, tripping because something else in the zone tripped the GFCI.  Therefore I prefer dedicated circuits for freezers, and try to find a way to omit the GFCI.   

Using receptacles for lights is perfectly reasonable - most of my installations are this - but all mine are located on the ceiling.  Luminaires are allowed to connect with flexible cords, but only within reason - I don't think the inspector would approve an arrangement which invites cords (or gasp, extension cords!) being stapled to the wall or draping across workbenches. 

Where you see knee level switched receptacles for lamps, that is a cheap method used in newer housing stock, and is intended only for floor or table lamps, not ceiling-hung lights.  

If you are not putting lights and receptacles in the same place, you can divide and conquer - install the lighting circuits in one project and the receptacles in the other.