I can answer part of this. I use two BES's. I have a work 3.6 server and a personal 4.0 server. E-mail is wirelessly synced with both. Now this is the part that gets tricky. With 3.6, you can only sync your calendar with one server. I'm not sure about 4.0, and I won't know until my work server is upgraded. With 4.0 you get a new service book (SYNC). So, it may be possible to sync with multiple BES's if they are both 4.0. Blackberry wireless sync heaven
Before you connect with the second desktop, make sure you change the default service book name on the first one from something other than 'Desktop'. I think it's on the advanced tab of the redirector.
Hope this helps,