This is the 1st step to running apsim on the PBS clusters at UQ, which has a "whole machine is allocated to you" paradigm.
Condor can use this same paradigm, with the extra benefit of not having to download an apsim to the executing machine so many times. The apsimUI condor job generator should use the "threaded" scheduler in Apsim.exe, instead of just running single instances (ie one for each "queue" command).
The way it works is to generate a batch file with multiple simulations for each Apsim.exe invocation.
The condor side requiresd extra tags in the condor matchmaking process. Full details here: https://htcondor-wiki.cs.wisc.edu/index.cgi/wiki?p=WholeMachineSlots
In short, if you're already rolling your own submit files, there would be no change.
If you're using ApsimUI, the batch files generated will be different, and they'll be dedicated to our cluster in toowoomba.