Partitioning Question. How does it affect Windows, programme

Hey, im new to this forum with a question... (can be quite complicated - for me anyway - so bear with me).

I have 2 x 250GB Harddrives in RAID Mirror.
It is a Dell computer and so my C drive is partitioned by Dell into a couple of secret small drives, for Dell Symnatec System Restore, that are not visible in My Computer.

I want to partition my hardrive, how does this sound...
50 GB Windows (C)
100 GB Files, Programmes, Documents - Storage (D)
100 GB Backup - Image of D (E).

The thing is... Will this affect the MBR (Master Boot Record) and so make the Dell System Restore Utility not work - ive heard it can be quite picky.

Would this partitioning actually work? I mean i plan on getting Acronis True Image, so i can turn E into an Acronis Secure Zone for images of D.

Now say i get a virus and reinstall XP.

So i wipe C and D. Reinstall windows on C and restore D from E, will the programmes retored to D still work, i mean what about the registry?

Arent programmes intergrated with windows (ie HP software, Panda software as examples to what ive got in my windows folder now)?

So when i wipe C (and presumably the registry and all other files that my programmes have installed in there) and restore programmes they wont be able to find the files that were in windows folder and so not work?

Also where should the page file be?

As a help, could you tell me setup you have?

Sorry about soo many questions.

Thanks for any input.