Hi,
It sounds like you need to model the "end conditions" for your system. If the system ends with a flange going into a skid then I guess you need to model the flange pair and an appropriate amount of piping beyond that.
To find out what the loads are at the flange pair you can use a "connect node anchor" located between the flanges (where there would be a gasket) and this will give you the loads, moments and movements at the flanges which hopefully will be within the "tie-in flange loads" that you have.
If you are lucky, for your end conditions, on the other side of the flange pair as it goes into the skid, there will be an anchor. I call this a "battery limit", you are normally responsible for the piping up to the battery limit and said nozzle/flange loads. The skid vendor is responsible for the piping beyond the battery limit which is inside the skid. So you only need to model the skid piping as far as the anchor, nice and simple.
If you are not so lucky, then for your end conditions you will need to model some of the piping within the skid, so you'll have to get the piping isometrics and pipe support types and locations from the skid vendor (or go and do a survey of the piping yourself if you have access to the skid). You'll have to use judgement based on the skid piping layout as to how far into the skid you model the piping to generate representative "tie-in flange" loads from your end condition piping.
I hope that helps,
regards,
Winnower.