You are always better off putting Windows on the Fastest,newest,most reliable, drive you have ,so if these two drives are close in terms of what I just stated then make the 5Gig the active primary,the 20 the slave .
The 5Gig is just big enough for Windows, especially if for email and surfing , I would suggest making the 20 Gig for data,Temp files etc to minimize the amount of space used by extraneous programs on the smaller drive.
