I need some BIG help!! I've read a thread about this topic and still can't get it right!

I have an intel Mac running Leopard OS. To transcode movies, i'm using iSquint (sometimes I use VLC but I'll first ask for help with iSquint)
For iSquint, the "optimize for iPod" is checked, and then there's the option "h.264 encoding"- i haven't gone into the "advanced..." settings yet. my movies convert to .mp4 (MPEG-4).
I sometimes put my sd card into a reader and then insert that into the usb port. Sometimes I just connect to my computer using the usb "cable" that came with the instinct.
Either way, it always appears on the desktop looking the same.
Can someone please tell me what I'm doing wrong? I get the "sideloaded" thing when I go into TV, but then there's just a grey area where the movie title should be.
I really need a "step by step for dummies guide" to help me with this- starting at square one, please! Thanks!