Hi there James,
More info required for a definitive answer, but I'll try to help...
Email - are you using an Exchange Server, or just a local POP3 account, connecting to the internet? If the former, then it's easy - you have your desktop running constantly linked to the server, and your laptop can synchronise over the network, just like it would if you dialled in remotely. If the latter option applies, then they both need to synch seperately - the only advantage from doing it across the network is if you have ADSL, or T1 pipe etc, in which case it's much faster than doing it at home. You won't synch Calendar, Notes, Contacts this way however (indeed, you would only ynch them in the former case if they are setup to run off the server, rather than locally).
The key in both cases, is that you don't synch the laptop and the desktop to each other - they both synch to the server independently.
Files & Folders - Are you using Win2k or XP? If so, then it supports a concept called 'Offline Folders' which will do just what you want. If you are using an earlier version of Windows, then there is a product on the CD (I *think* Office, but it might be teh Windows CD - either way not installed by default I think) called Microsoft Briefcase. I'm hazy on the details, but I believe that this is basically a slightly less refined way of doing the same thing.
Hope that helps... Jonathan Challis
IT Manager