Well i tried a longer flight plan tonight, planned in LNM and imported into MSFS, however, it seems to have created two flightplans from the one file?
Anyway, I loaded it into the FMS and indeed it had created a mess, there was a pointless loop near the destination, I deleted and corrected that enroute just for practice, then added my arrival once i had ATIS online.
Then I played with ATC(built-in) and realised you cannot use VNAV with ATC it seems as the descents do not match and ATC gets all shirty about it, confirming my view about dumping the FS ATC, it requested I descend from 21000 cruise to 14000, then almost immediately requested me to descend to 16000 and expedite 
its a joke really.
Anyway the flight was a success, the passengers were happy and it was also the longest CJ4 flight to date for me. I cannot start the trial of Pilot2ATC yet as other matters mean I do not get much spare time so the trial would end before it started 
Edit:- Just looked at the plan in world planner picture and the notes i took directly after importing into the FMS - the odd loop was created by the FMS not the world planner import. The manual does state odd things can happen when importing.
In Pilot2ATC is it possible to create the whole flightplan or is an external app needed - Simbrief/LittleNavMap etc ??