L2TP/IPSec is not integrated with any of the SBS wizards. Though manually configuring a PPTP VPN is still quite simple, a L2TP/IPSec is quite a bit more elaborate and you can have problems with client machines and NAT when using IPSec and Server 2003 SP1 and newer. These days a proper IPSec VPN router is so inexpensive most people wanting more security than a PPTP VPN opt for a hardware device. Moving the VPN server to a router is more secure in that users are accessing a perimeter device and not your domain controller directly, more secure in that it uses 'full fledged' IPSec, more efficient in that you offload the encryption service to a dedicated device, and allow more access control. An ideal unit is a Cisco ASA5505 which starts at about $400, or if the budget is limited you can get a Netgear FVS318 for $150, or a Linksys/Cisco RV042 for $200.
If interested in L2TP/IPSec the following article outlines the basics. It is for server 2003 but the process is very similar for 2008.
http://technet.microsoft.com/en-us/library/cc787915(WS.10).aspx