Hi,
Ah, I've had a look for homesite and see it's a code editor by Macromedia. I would be 99% sure that it will use ftp to transfer the files up to any server as that would be the only protocol used for file transfer up to virtually all web servers. Certainly, all other Macromedia products (dreamweaver, ultradev etc) use ftp for this process.
Don't know if the app gateway will fix the server error but a guess would be that you may have some non standard authentication method for logging onto the ftp server - make sure that you haven't got NT auth (or whatever the equiv is in 2000) but plain text for regular ftp uploads. I recall that the original w2k implementation of the kerberos authentication method was, ahem, "extended" so that only MC clients would work (though I think this was addressed later) so this might not work either if you're using that. (I know your client machine is an MS box but as the gateway is NATing the local network behind a single IP address, the ftp app gateway will be acting as a proxy on behalf of the client PC).
With regards to the pcs appearing in the network places. Computers in that view are there if they are identified via subnet broadcasts - so you only ever see them when they are on the same subnet. One way around this is to reference a WINs server on the other subnet which will bridge the gateway.