Hi,
I am not sure there is an upgrade path from SBS to Windows 2008. I believe there is an upgrade path to Windows 2003. Here is a link for your reference. However, I could be wrong and if I am, someone will give you better information.
http://support.microsoft.com/kb/555073/en-us
When you are on Windows 2003, here is the guide to updgrade to 2008.
http://support.microsoft.com/kb/951041/en-us
Once you are on Windows 2008 and Exchange 2007, having the applications on separate machines is fine. I think this is common and most run in that type of environment.
You may want to consider just doing a clean install of Windows 2008 on the new machines and then setting up your software fresh.
Here is an article on migrating SBS to Windows 2003. There is quite a bit of information about the migration upgrade paths etc. on the internet. There appears to be some effort associated with this type of upgrade or migration.
http://tec-articles.blogspot.com/2008/01/migrate-from-sbs-2003-to-2003-standard.html
