The two issues are unrelated, but I'll answer both:
IPSec VPNs do not traverse NAT, so you will need a firewall capable of setting up the tunnel at each site. You've given no indication on whether your current firewall supports this functionality, so you may need to look at getting a second firewall of the same brand, or you may have to look at replacing the firewall. Regardless, your IPSec tunnel will exist separately from your SBS server.
To answer your second question, yes you *can* set up authentication to traverse the VPN link, but generally speaking it is slow and logon times will be poor. If at all possible, it would be better to set up a second server at the remote site and make it an domain controller and use the AD tools to organize your sites appropriately. This will provide a much better user experience.
For applications, you can always set up a terminal server so that heavy network traffic does not have to traverse the WAN.
-Cliff