can isite track scpc satellite

I am not sure what you are saying when you say "Use the 3100 to track."  Do you mean receive the SCPC downstream carrier with the 3100 and then transition everything to the 5000?

As you are probably aware, the 3100 cant do an iSCPC termination (point to point/hub-spoke).  So using it as an end point as an iSCPC spoke is not going to happen. I dont even think that 3100 board will take the iSCPC software, I believe it is incapable of retaining it.  I am not sure if you can use it to recieve the carrier either as an iSCPC downstream carrier is a little different than a TDM/Downstream carrier. I would ask iDirect if the 3100 can be used to check receive.  

Is your other end point going to be the teleport earthstation antenna or another remote site?

If I were you I would use that 5000 from the start but if it is your only operational modem (right now) that may be a concern for you.  Either way (using the 3000 or the 5000) there is going to be a service interruption as you transition from D-TDMA to iSCPC.

That 5000 will require a new (iSCPC) software image and you will need your new SCPC transmission plan (if changing space segment or Xponders....for all we know, you may be staying put in the same MHz that you are presently operating in).

Just make sure you have all the information and software readily available to make the transition smooth.  Poor planning could result in extended downtime.