I have two shops, my other was was already fairly ecclectic but all art based, although I have stretched that from prints and cards right through to art dolls. Anyway I decided to also do handspun yarns, something I have always loved doing, and there was just no way that was really going to fit with my art shop (suzyjaneb.etsy.com), so I opened my WoolWench shop. I have to say its not always easy to manage both, simply because I feel bad if I am favouring one over the other and 'neglecting' one - in fact the my yarn shop is already doing much better than my art shop, so my tendancy is to focus on that more.
Basically I use two browsers, one for each shop, that way I stay logged in and dont have to switch all the time, and I have everything related to each shop separate (facebook twitter etc) so I also dont have to switch accounts and logins, just open the other browser :)