I hate the command line... but it can do a LOT more/faster Folding than the standard graphical version: it can run both your CPUs, and it can help you get Work Units that are optimized better for Macs.
What to do? Use InCrease. You never have to TOUCH the command line. InCrease handles ALL of it for you--so you get graphical ease-of-use, with maximum folding power. I'm glad I finally tried InCrease.
And for "expert" folders, there are lots of extra options.
A tip for modem users: want to keep your Mac busy even after a WU ends? Run more than one unit--even if you only have one processor! Both will run at half speed, but the same work gets done in the end, and if one WU ends, the other can keep going until you next dial in for fresh work. I have run up to 7 units at once on my eMac when I went away on vacation and wanted to keep it busy for a week. (Not to worry, they all made their deadlines when I got back.)
Also, here's an up-to-date list of folding tips if you want top speed:
PS, re "fpd," that's the molecule viewer that InCrease uses to display the 3D molecule if you wish.