Ragnarok's guide to powerups!
1) Deciding how many powerups in the level:
This often depends on the scope (duel sized or 7v7 etc.) and style of the level. If you want action packed gameplay, then put more powerups in my opinion. If you want a level more about control and taking advantage of spawn times etc, then I'd go for less powerups. There's no harm in placing two of the same powerup in one level by the way, so never shy away from that idea if you feel the need to do it.
2) Deciding what powerups to use:
Well this is something I usually do while making the level, and it's difficult to strike a balance if you want different powerups in the same place of the mirror image of a symmetrical level. You have to design the level to suit that. So pick powerups that you think will be strong in the level, and that compliment the layout. So for example, I place bouncer powerups opposite to RF powerups because I put a varying amount of slopes and large horizontal corridors to somewhat balance them out. If your level has lots of fastfires, then why not throw in a blaster powerup? If the level has an emphasis on seekers, then throw in a seeker powerup.
3) Deciding where to place powerups:
Powerups are usually placed away from other areas of interest of the level (i.e. bases or carrots) or have some sort of thing preventing you from getting them immediately after doing something, or killing two birds with one stone by camping in one position. While I don't mind them being relatively close, my point is just not on top of eachother.
Next, you wanna know where to actually place them in the level. I tend to put the stronger powerups like Seeker PU around a difficult place in the level, so it's not easy to get the powerful gun, or I make it very central to the level so everyone can get it (usually not the latter). Where specifically to place them? Well, I tend to put powerups in places they work best, so a bouncer PU near thin walls so you can shoot through the walls, or a toaster near open space, or RF in long corridors. Alternatively, I also like putting strong powerups in choke points, like small dead ends (nothing too drastic) as people are bound to camp there in bigger levels and what better place to kill campers than in a small dead end?
4) What to do once you've placed the powerups:
I'd usually throw some ammo around it, make the layout or eyecandy look like something of interest spawns here, or at least throw some ammo around it in a cool shape to signify something spawns nearby. And furthermore, if you're ever gonna place a blaster powerup, please just throw a load of fast fires next to it, noone's bothered to walk around the level and collect them in most cases.
5) Finalizing your decisions:
Well, I find when I make levels, some powerups end up being overpowered in certain levels, like bouncer in most of my levels (probably because of how I make them). To counteract this I sometimes just remove the powerup and change it for something else. Or swap it for another powerup in the level to change their placements if it makes the level work better.
Hope this helps at all, but uh, I wouldn't know I haven't made levels for a while now.