I can't believe what I'm hearing BM.
Of course put your OS/Apps on the new drive. The OS will be much more responsive and will startup/shutdown faster. You should use the 5400RPM for storage because it is slower. Storage is mainly there for just that, storage. What's the point of having a fast 10K RPM drive and let files sit on it doing nothing all day? What a waste of speed. Or even better yet, put as much on your fast drive as you can, and use the old drive for storage, but put your least accessed files on the older drive. That will optimize space and speed.
I would suggest creating a separate partition for your OS. This will separate it from the rest of your files, and help cut back on fragmentation of the OS.
What you can even do is split the swapfile between both drives. Put a certain amount on each drive. Yes you can do that.
It is a little more work setting everything up, but it will help in the end.