Wait, hang on - I'm not sure I've understood you. You say each time you select a new server you need to enter the credentials again - SQL Compare can't tell if you use the same credentials between servers, so you won't be able to make it autofill credentials for a server it hasn't seen before.
If you only have SQL authentication on your servers, I'm afraid you'll have to enter the username and password every time you start a new comparison. If you're commonly comparing a certain pair of databases, though, you can save the comparison as a project, and if you ticked the 'save password' box while setting it up you won't need to re-enter credentials for that comparison.
Does that answer your question a little better?
Andy Campbell Smith
Red Gate Technical Support Engineer