Here's how I've done it...
The way I've done it is just to run a small FTP server (there are ton of good free ones out there) on my home Windows PC. Then use a free service like
DynDNS which basically just gives you a web address name so you have a way to access you ftp: server. So something like
ftp://miby.dyndns.com or whatever name you chose.
Once you have it setup so you can see and access your files over FTP: then what I use on the work PC is program called
WEBDRIVEWebdrive basically lets you mount an FTP site as a Drive letter in Windows. So you can make your FTP: site with all you Amiga files the H: drive or whatever you want.
From there as far as your work PC is concerned it thinks it's just another HardDrive and you configure WinUAE just as you would just pointing everything to H:/WinUAE/ROMS etc or whever you put your files.
Works pretty good for me. Webdrive is pretty cool, but you do have to pay for it. Haven't found any free alternatives. Of course on the Amiga we had programs like this for free 10+ years ago with a program called MountFTP. Amiga was again WAY ahead of it's time in this area. :-D
EDIT: Just read the part that said you wanted to do it with the tools you have :-) Well, anyway, if you don't find an easier way, check out WebDrive.
