No offense, but you seriously need to learn AE's basics first. You're treating it like you were working in Photoshop or like an edit suite, depending on what you want it to be most for the moment, but none of that reflects actualyl what AE is - a compositing program. Let me clarify:
everytime I try to seek forward to make changes it takes forever and I see a status bar loading each time I switch Frames (it has to load each frame I seek through and there is over 2000 frames).
Yes, almost nothing in AE is realtime. That's why people need to create RAM previews for realtime playback. Perfectly normal and in your case you are probably complicating the situation by using compressed formats where in order to show a given frame, several additional frames before and after need to be decoded. Fuirthermore, you may simply work off a slow drive.
The machine I'm running is a hp z600 workstation with 2 xeon quad cores and 12 gbs of RAM with a 2gb video card, so I'm sure the PC isn't the issue.
As per above - it likely isn't, but it's your wrong perception of AE and your wrong approach to the matter.
also, is there a way to only have the edited areas be visible for certain frames,
Yes, you split and duplicate layers. pelase refer to the online help for basic procedures on layer management
will splitting / duplicating layers help me with getting the clone stamp blotches out when it moves? I have tracked the motion on the clone but am just having trouble with what to do next in making my previous clone invisible after what it's covering up is off the screen.
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Yes, you split the layer and only paint/ clone on teh segments where you really need it. All other segments will be unaffected or you can remove the paint strokes by untwirling the properties in the timeline. Any effect will obey the temporal bounds and in strict terms painting is just that - it cannot extend beyond the invisible, at least if you do not make use of offsetting the clone source point in time. You might wanna have a lokk at the help for some deeper understanding. There are also some tutorials on creativeCOW expalining basic cloning that came out around the time of CS3. They may be old, but are still applicable to your situation.
excellent thanks. I have been reading up as much as possible but will probably look for some video tutorials once I can find some headphones. Im interning at a local company this summer and the graphics guy resigned so I've been pulled from my IT work to learn 5.5 on the go.. Thanks for your timely responses and input.