I have found a few solutions to this dilemma, I figured I would share for any who have a similar question.
When inserting a new Bill of Materials into a drawing you do not have to select a view that is in the current sheet, you can also select views from the Feature Manager Design Tree. This means you can effectively have the same Bill of Materials on every page of your drawing and simply hide the rows that are not relevant to the subassembly on that page without effecting the numbering.
Another solution is that you can add a Bill of Materials to the Assembly itself, tweak it to look the way you want it (reordering parts, etc.) and then, when you insert a Bill of Materials into the drawing you can select a view from the Feature Manager Design Tree that contains the assembly, and then select copy BoM, and select the BoM that you made in the Assembly. Again, hiding the rows that are not relevant here.
A third solution is to use the split BoM feature and drag the derivative tables to the appropriate sheets.