Alrighty... here we go again! 8)
what do i need to take note of when upgrading pickups?
You want tone above everything else. That's most impt... a pup can drastically change the way your guitar sounds so... be very very hardworking, go research as much as possible on the pups you are eye-ing. Tone is relative... but in general, for starters, you might want to go with the flow and choose one of them "safe" bets... eg Dimarzio Breeds. Then from there you can fine tune once you have a better grasp of what tone you want.
do i need to like..match different pickups' outputs? like those with diff power can't be put together on the same guitar?
Ideally, yes.. match the output... but there's no hard and fast rule. I matched a Dimarzio X2N (510mA output) with a Dimarzio Humbucker From Hell (226mA ouput) before... thats more than a 250mA difference and I balanced their clean volume output. The only problem with matching low ouput pups with hi output pups will be... when you switch from either one, you will note a change in saturation (only when playing with gain) but there will be no change when playing clean. So in the above case, i was rip roaring with the X2N , switch to HFH and it turned into blues.
SOmething to note, DC Resistance is quite impt when you are running pups in parallel... if you have a Dimarzio TOnezone (17k DC) with the Dimarzio Humbucker from Hell (5k DC), when you wire them both in parallel, you'll notice that you have bascially a HFH tone... why? Because current flows to the lowest resistance... So if thats a concern for you... match DC as best you can... like 10 and 17 or 12 and 14..
how do i know which pickups to choose in which position?
No rules to this. Generally pups will be labeled for neck or bridge.. but some ppl like neck pups in the bridge (like me, Dimarzio breed neck in bridge) and some like it the other way round. Some like the same pups in both positions.... Paul Gilbert has used Dimarzio Tonezones in both positions... PAF Pros too.
Have fun. Once you start on pups... be prepared to spend.
The better tone is always out there.