Choosing New Sequence Type?

Hi all, I'm just getting to grips worth Premiere Pro CS4 and really loving it. I understand much of the interface and editing features and have even mastered Adobe Encode to 720p for Youtube HD playback. I have two queries I'd really appreciate some input on.
1. What still baffles me is starting a new project and selecting a 'Sequence Type'. All tutorials (even my beloved Lynda.com) really skip over this in ALL FOUR training sets!
I can take the raw video and put it through Encode and upload with good quality video even though it isn't quite HD to start with (I'm recording in-game action at half size so 960 x 600 30 FPS and 44KHz audio).
Using Adobe Encode it recodes to the right resolution in great quality though a little soft as I'm presuming it's extrapolating pixels to fill the space difference from 960 x x600 to 1280 x 720.
But what Sequence Preset should I choose to work with? Should I create a custom? All desired output is going to be Youtube 720p.
2. Also, as I'm recording at half screen-size, that means my true resolution is 1920 x 1200 so a little over 1080p of 1920 x 1080. Is there a way I can see if my pixels are square or is there a better way to use this full screen in a 1080p resolution without cropping edges (also Sequence Type I should use?).
I mention pixels thinking if they weren't square and were made so it might decrease the resolution enough to fit in 1080 lines but I might be mis-understanding this bit?
Many thanks in advance.

Upscaling, at any level, is going to cause issues, as you have mentioned - pixels must be constructed, where none existed - Interpolation.
Personally, I would leave the source footage alone initially, and choose the Desktop Preset, setting each attribute to match your footage. Edit as is needed, and then Upscale for Export. If at all possible, I would try to keep the Scaling algorithms out of the mix, until the end.
I may just have missed it, but what is the CODEC used for your capture footage?
Also, if you are doing video screen-caps, you have square pixels, as that will be the PAR of your computer screen.
Good luck,
Hunt

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