Unfortunately there is no way to connect via the API to multiple FEMAP sessions. This is a limitation of COM rather than FEMAP. COM always connects to the first instance of FEMAP that you started that is still running.
Multiple models in the same session however can be accessed. Refer to Chapter 3.16.1 of the API manual ... Model Activation and Management. This will provide you a number of methods to find the models that are available and to activate the one you want.
I should add a slight caveat to my previous post... while it is true that COM always connects to the first instance of FEMAP, if you are using the API from the embedded API Programming window, and you access the object using the default syntax...
Dim App As femap.model
Set App = feFemap()
then the API will access whichever FEMAP session it is being run in. Unfortunately, as I said, this is simply a feature of the embedded interface and is not available from outside the FEMAP environment.