If you are using purchase agreements and also rely on master planning then you might want to look at the parameter in master planning called find purchase agreements. The way this works if you have a planned purchase order that is suggested from master planning when it is firmed if the parameter is not enabled then the price is picked up from the default price of the item so if you have purchase agreements they will be ignored. If you enable the parameter then it will check if there is an agreement for the item from the vendor that is the default vendor for the item and apply that to the purchase order when it is firmed.
Here is a quick overview.
AX2012 R3 CU11.