Can't give them names??? You mean you never used the alt-name field? Works like a charm. Wing name appears at the top and ship name appears right under it. Only drawback is you don't get to see the ship class.
1) That's a pretty obvious reversal of the way round it should be.
2) You can't put the correct name on the escort list that way (And capships should always be on the escort list as far as I'm concerned).
3) The event log will refer to the ship by the wrong name
4) Any messages will have to be sent by #name instead of the real name or they'll appear with the wrong name. Even if you do this you won't get the targeting bracket around ship when it sends a message
5) If you are killed by that capship the wrong name will appear in the "You have been killed by..." message.
Now I know those are mostly nitpicks but for me I'd consider a mission sloppy if it had any of those errors in it unless they were unavoidable. Admittedly I've very picky about my FREDding and you might not care about any of those problems so it's completely up to you how you FRED your own mission.
I am after all the sort of person who gets really pissed off that the Belissarius shows up as Self Destructed in the mission log rather than Killed By Psamtik.