How to update safely to new version?

[domainkiss]

Currently I have vb suite 4.03 and I want to new version 4.04 patch 1.

How to update safely to new version?

I have vbseo 3.5

I made many changes in default style (css files and other templates)

And I made changes in functions_socialgroup.php and forumdisplay.php.

Here are questions:

1. Shoud I upload first version 4.04, install it and then upload version 4.04 patch 1?

2. How do you update? Do you send all files everytime when there is new update or just particular files?

3. There is something new with creating templates in 4.04. Is my template safe?

4. If I shoud upload all files from "upload" folder... Can I automatically "update" files functions_socialgroup.php and forumdisplay.php? Plugin or something?
For example...
I changed "Nasty Query In forumdisplay.php" from:
http://articles.digitalpoint.com/content.php?r=7-Optimize-vBulletin-4

Please help:)