if you keep your stuff neat and put away, it's not hard to keep things separate. In order for me to play electric guitar, I have to pick it up off the wall, go get a strap, get a pick and tuner from the rack drawer, grab the amp and power cord, and then some instrument cables and whatever pedals I want. After all that, there's no way in hell I'm going to want to pick up a mic, stand, cables, and then power on my recording equipment.
You think you work best when everything is within sight, but if it's in your mind(keeping stuff ORGANIZED and not just neat), then you won't have a problem.
Lighting is a personal thing. For the most part, I just use the 3 lights that were already on the ceiling. If I want "mood", I turn off the ceiling lights and only use a small desk lamp. Been thinking about picking up a standing lamp and putting in some colored bulbs, but I'm rarely ever in that mood. The soft desk lamp is enough for me.
Plastic tubs are great. I have a few sprawled out around the apartment. Mostly they just end up as storage units with a "table top"