I have a design with a multiple instances of large Analog macros that have built in IO's. They need to be in placed in specific locations in thepadring of the design. Does anyone have suggestions on how to implement this in an APR flow?

In the Magma BlastChip flow - for versions beyond 3.0 - you can force the cell
to be of type pad, and you should be able to place it via the "force plan pad"
command and "run plan create padring $m -noroute", along with the other pad cells.