First off, any time you try to patch together a couple of systems to achieve an added function, it's not going to work as well, if at all, as migrating completely over. I don't think 3Cx was really designed to be an add on to another PBX.
That said, you should be able to add incoming VoIP trunks to 3CX from outgoing VoIP lines from the current board. And in reverse you could also add incoming VoIP trunks to the 5000 from outgoing lines built in 3CX. By building incoming and outgoing routing plans in the 3CX you might be able to get something working, perhaps not well, but...
If 3CX offers features that your current system lacks and you currently use SIP sets( one of the big expenses), i would look at putting together a 3CX system and then, after some testing, move the whole office over to it.