Don't worry about 'setting' any suffixes. They work on their own accord. If both systems are on the same subnet and have NetBEUI loaded, you should be able to find each other using broadcasts. If your W2k system also has other protocols loaded, you might want to check your bindings as well.
If you need to, you can edit the lmhosts file on your NT system and add a single standard server entry for the W2k system. Don't bother with creating any non-computer mappings. And get rid of the '.sam' extension on the file.
Another thing, are you sure the vendor's app uses NetBEUI to look up things? I think it's more likely that it uses NetBIOS names to look up things. In that case, you don't need to have NetBEUI loaded as a protocol at all, since M$ uses it commonly within the context of TCP/IP. I would get rid of NetBEUI, create an lmhosts file, and start from there. Also tell the W2K server to enable NetBIOS over TCP/IP for that adapter.