I did the same thing a few months ago and had the same concerns, the SO Entry, Invoice and AR Customer panels were already customized. I did not want to take the chance the TC.M4X import would override my existing custom panels. I asked TC for a .M4X file that only contained the UDF's and UDT's but they were not able to provide that.
So, I imported the TC.M4X to my local install, then exported their UDF's and UDT's, imported to the customer installation then manually created the panels and added the TC UDF's/UDT's. Did not take too long and figured it was better to safe than sorry.