The main thing to be aware of is that godaddy like many hosts enforces a medium trust security policy, and this prevents us using our VirtualPathProvider to load the theme.skin file from the skin folder. you can work around it by copying your theme.skin file from your skin folder into the /App_Themes/default folder, but you will need to remember to do this after every upgrade of mojoPortal. It also means if you host multiple sites in a single installation all sites will use the same theme.skin file
Note that if you are looking for better hosting, Arvixe hosting is full trust so you won't have this issue there.
Hope it helps,