Lets start with theme's. Once you are able to ssh into your iPhone and add theme's. Its just a matter of finding the correct location to change Keyboards. Dialers, ect...
How to SFTP Winterboard themes 2.0
1. install OpenSSH
(from list of apps available from Cydia)
2. install winterboard
(from list of apps available from Cydia)
3. Get a SFTP program to SSH to your iphone from your computer
(MAC
FuGu--
Wiki Guide / PC
WinSCP--
Wiki Guide)
4. SFTP settings: Server will be your IP address of your iphone, User = root, password = dottie or alpine.
(get your iphones IP address from Settings->Wifi->click the arrow next to the wifi network you are connected to. you'll then see your IP address)
5. Winterboard themes go in /Library/Themes/ , this is the directory you'll place your themes. each theme should have it's own folder.