Good to hear from you. Actually, we have just implemented what I hope is the best solution! We can either import the analysis files (group compositions and ordination) with header AND labels or without header AND without labels. PATN will auto-detect which. Yuo will not be able to mix the two forms.
This will be in PATN V3.02. We have closed off development on v3.02 and have just to complete the help file and a little further testing before release. We want to get this out as quickly as we could. Consequently, we will have to leave some features to v3.03.
In relation to the export of colours, the ordination coordinates ARE the colours (x=red, y=green and z=blue). You can export these as is of course. If you need them in the range 0-1, either use Excel or pull them back into PATN as data and standardize them!
Hope that helps.