Since I kinda joined in your original Post a bit after you got started, I stayed away from 'addressing' it (per se.) What I mean is I kinda 'picked up' where I jumped in.
I would have recommended a latex-based primer, and I would have recommended a 2nd coat wherever you spackled. Oil-based paint wasn't really necessary and I'm sorry you had to endure the ill-effects of said Primer. Anyways, unless you're top-coat is oil-based, you can use Latex Primer with a Latex Top-coat.
Now, to answer your question here. Always prime at LEAST once, preferably 2x's when you have NEW or spackeled drywall. Another time you Prime is when you don't want what's 'underneath' your top-coat to 'bleed through' from below. Like going from a dark colored wall to a light colored one, or when you're repainting a wall that has some waterstains. As the can says, the Primer is a Sealer. As for your particular situation, yes, you're OK to have Primed the area that you did. Preferably 2x's (again.) IF the rest of the wall is LIGHTER than the color you're putting on, you needn't prime. BUT, if it's DARKER, prime 2x's. AND, to boot, after the 2nd coat of Primer/Sealer has dried, plan on putting on 2 coats of top-coat. It's just a rule of thumb for me. IF, for example, you need 2 cans of paint to paint the entire room, you don't necessarily need 4 to get through 2 coats. Since the 1st coat get's 'sucked into' the Primer/Sealer, usually, you can get away with LESS on the 2nd coat. Go ahead and buy more paint than you need. Just be sure you can RETURN what you don't use from an UNOPENED can. (Ask at the Paint Desk or Customer Service.)
As far as getting 'good' at it. When you're finished this job, you'll be all the wiser. As I mentioned, the 2nd coat (primer OR top-coat) should go on easier/quicker because you're painting over fresh 'paint' when you do the 2nd coat. IF you're not sure where all the 'spackeling' was done, do the entire wall with Primer. And even though you have pinholes, use a roller; not a brush. As for painting latex over oil, that's OK in the Primer stage. (It may be a different matter if you're painting latex top-coat over an oil-based top-coat ...)
Hopefully, I've answered your paint question(s). 10-4 on the sub-floor 'thing'. I'll be around as will be others if you have more ?'s. Steve: may not be - I believe he's gone fishing. My best to ya and hope this helps.