In general you just need to pay a bit of attention to detail to get it under control, once for each new library or SDK or combination thereof you get to deal with.
I dug up a small reference document I wrote some time ago, and added to it how XNA handles matrices since I am doing a bit of XNA development.
It is not complete so if you would like to add to it I will gladly send you the OpenOffice original.
If you find I wrote anything wrong please let me know.
