Firstly, what system are you using that you would need to integrate into vBulletin? There may already be modifications or tutorials that would do or show you how to do the required changes...
Secondly, adding extra fields to the user table should not cause any mess-ups - It is recommended that if you are going to alter the default vBulletin user table, that you use a prefix or some other way of ensuring that in future versions of vBulletin you don't get clashes between your fields and the possible new user table fields that may be added...
For example, creating a field called "option1" may cause issues if the next version of vBulletin also has a field called "option1" - Therefore by calling your field "site_option1" you avoid clashes
Chris