I've got two OFP CDs. Does it make a difference which CD key I use with either one?

No. If you're installing OFP on two separate PCs, using two original CDs, it makes no difference which CD key is used for which installation.

However, it is illegal to use the same CD key for more than one installation of OFP. Furthermore, if you do so, you might trigger FADE and this may be detected during multiplayer games and automatically force you off the MP game server.