Your 3550-12G switch is already doing L3 switching (routing) of IP if you can ping and RConsole from the employee network to the server on the school network. And you're sure that those two networks are distinct VLANs, each with its own IP network or subnet address range.
It will probably not help you to put the school server's switch port into both VLANs. That switch port would then be trunking VLANs, which would require your server to have a network adapter capable of handling 802.1Q-tagged VLAN traffic. You would also need Novell-specific drivers for that network interface card.
If you're trying to get some sort of administrative control over the school NDS tree from the employee network side, this is more likely a Novell-specific issue. It's been over 10 years since I dealt with NetWare 4.x and NDS as a former CNE/CNI, so I've forgotten much of what I used to know.
Seems like you need to somehow join the school network's tree to the employee network's tree. Terms like "pruning" and "grafting" are coming to mind. You would probably want to do this in such a way that the employee tree is positioned as the dominant one, and the school tree is just a branch.