Firstly if you go to your bom the row numbers will show (see picture below where I have selected row 6) and by keeping the left mouse button pressed and selection the row number you can drag this row up or down the bom to position it where you want it
Then lets say you only want to see the top 4 rows you then right click on the "5" of row 5 and and then go to split from the drop down menu and then select "horizontally above" from the side menu (see picture below) this will now split the BOM into 2 parts. You can then drag the part you don't want off the sheet and leave it there or you can delete it.
Note sometimes it can be handy to leave the unwanted part off the sheet as if you change your assembly by adding more parts you can these will be added to the bottom of your unwanted list, you can then bring this back onto your sheet and merge it with the other BOM, move the rows as needed and then split the BOM again.
Another way to stop a part appearing in a BOM (but I am not sure if it will work in your situtation of having various configurations) is to right click on a part in the feature tree of an assembly and select "component properties"
Then select " exclude from bill of materials" to exclude that part from the BOM