Forefront Protection 2010 builds on top of Exchanges existing ability's. Adding extra antispam capability (such as using the cloudmark antispam engine) and other facility, such as Antivirus and Antimalware.
Control of the antispam features present in Exchange is integrated into forefront, so they effectively become a part of forefront when installed. As far as the junk mail folder is concerned, I believer Forefront will automatically place mail into the junk folder if it has a moderate SCL rating (so 5-7 I think), anything over that is deleted or quarantined. The cloudmark engine is supposed to be much better at categorising mail, so you should not see many mails with SCL rating in that range, they should either be low, and in your mailbox, or high and deleted.