There are different methods of installing and using Custom Themes on which I will get to next; (all have their pros and cons!) In the end its your choice with which method you want to go with.
However both methods #1 and #2 make use of modifiying the app.db file which makes the themeing temporary and failsafe. Once the Database gets rebuild, your custom modifications will be gone though!
Method #2 - Manual Icon Themeing
[Tutorial] How to install Custom Themes manually (3.00 - 3.52)
|- every icon can be customized
||- every icon needs to be changed manually
||- not permanent
Method #3 - Overwriting activated theme files (FW 3.30 - 3.52, 3.60)
The trick here is to activate an original theme and overwrite the decrypted and temporary stored theme files in the ur0:shell/theme/ with your custom icons.
Your theme will stay permanent until you change the theme via options!
|- permanent themeing
|- no database modding
||- everything is gone when deactivating the theme
Note: If you are on lower firmware and got no original theme installed already, you can't make use of this method.
Tutorials & Guides Compilation
[Tutorial] How to create custom Vita Theme Packs [for Method #1] (via hackinformer.com)
[Tutorial] How to fully customize PSP/Vita Bubbles + LiveArea
Custom Vita Themes Database (via hackinformer.com)
Frequently Asked Questions
But the e-mail app is present since FW 2.00, why doesn't it work for 2.02 for example?
Some essential changes were made in firmware 3.00