I just went and reviewed my fabric scans as I couldn't remember how big I made them. Most of mine are three inches square, 72 dpi (screen resolution).
EQ6 does tile fabrics, so if possible I try to capture a repeat in the design. If it is really important, I'll save a much larger piece of fabric to the Library for a project, however if larger pieces of fabrics are used a lot, then the program can start to slow down as it gets too big.
Also, remember to crop off any white areas in your saved scan or they will show up as part of your fabric.