This feature is maddening. There is no consistency with the method of mating and positioning of parts in an assembly, when I get one mate in place and add another the part flips upside down or does other goofy things, then when I change the position using the X,Y,Z tools it does away with the mates. Am I doing something wrong?
Are you talking about the Move/Copy Body command? In that command, you can either use Constraints (mates) to position the body or Translate/Rotate; you can't use both at the same time so that is why it does away with the mates if you switch methods. That is why it is a button instead of two tabs in the PropertyManager, so you switch between the two methods trying to imply that it is not applying both methods at the same time.
When using constraints/mates, then you need to create all of the mates that you want within the single Move/Copy Body feature. In this regard, it is different than assemblies. In assemblies, you make a whole collection of mates that are put in the mate folder at the top assembly level and they are all solved simultaneously. In the part, all of the mates in a single Move/Copy Body feature are solved simultaneously. If you make a 2nd (or 3rd or 4th) Move/Copy Body feature, then they are solved sequentially, with each of the mates within the 1st one solved first, then the ones in the 2nd feature solved 2nd and so forth. This is the nature of parts; they are sequentially solved. So any mates in later Move/Copy Body features will override the ones you've done earlier.
So, are you creating all of your mates within a single Move/Copy Body feature and they are not working as expected? If so, I would suggest posting a specific example to be looked at.
-Jim