No problem. The only thing is that once you start having one partition with all your documents and apps, the other will be missing some of them, and then you have to remember where things are.
I have 2 drives in my MBP, one with Lion and other with Snow Leopard.
The Lion one is an SSD 256GB and the Snow Leopard one is 1TB.
All my photos, videos and music are still in the Snow Leopard drive and no problems at all, just my disorganization with the data.