Should I Export Multiple Clips or Make One Giant One?

I have just started to use FCE 4, and love it.
However, I am running into the same problem as many other people, but can't seem to find the answer to MY question...
I am editing a HD movie imported via FCE from my Canon HG10. I use the Magic Bullet Looks video filter on my video.
My question is...
Since it seems that every time I do some small change to the project (text edit, transitions, etc.) it has to re-render the video effects with it (taking about 4 hours each pop).
Is it better if I edit each video clip with the filters in a seperate project, export those clips, then add them back to the entire project? Or am I missing a key step in making this all work in one large project, efficiently?
Thank you for all your help.

Michael Trauffer wrote:
Where are you storing your source media?
My source media is being stored on a Firewire 800 external drive. I realize that will cause some slowdown, but it shouldn't be that much, should it?
Are you using SafeRT or UnlimitedRT?
I don't know what those are, sorry.
Having to render constantly leads to a couple of different possibilities:
1. Your source codec doesn't match your sequence settings
How do I check that?
or
2. Your real-time playback capabilities are limited by your system setup.
I know for a fact that applying a Looks filter to any clip will require rendering. The time it takes for a render depends on your system and where your source media is located.
But it keeps rendering the same video, even if I make a change to another video track (like a text track).

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