I'm in a similar spot, to the extent that I listen to Lossless files at home but need MP3s for my iPod or the MP3 player in my car's head unit. For how much space it takes to store MP3s, comparitively, they're not a lot of extra burden. Also, since I'm using LAME to rip to MP3, conversion times are pretty slow.
I've opted, for the time being, at least, to keep both in my iTunes library. I created a smart playlist that shows only my Lossless files and is just as easy to browse as the main library. And a smart playlist of MP3s for the iPod and audio streaming around the house. I'm not saying it's the most graceful solution, but sorting by kind makes it actually very easy to play or transfer the correct file. There are more complex solutions out there, but this at least has KISS on its side.