You must allow Perian to completely finish loading/converting the video before it will allow settings to be modified.In Quicktime go to Window->Show Movie Properties (command + j)
Then, select "Video Track 2" (it must have "Text Subtitle" as Format), go to Visual Settings and edit the Scaled Size to font size and Offset to reacomodate the subtitles.
Quicktime X doesn't allow modification of tracks in that way; you want to do the optional Quicktime 7 install (it's on the OS disks, or you might already have it--the player is in the Utilities folder, not Applications) and modify it from there.
Although I'm not actually positive you can do that if you don't have QT Pro, which isn't free--I haven't personally used a system without Pro for a while. Regardless, the previous instructions assume QT Player 7, which isn't on Snow Leopard by default.