The way to go is to create a new part for each value.
You can do this easily in the part library editor by selecting the psrt, RMB and copy part, then paste it in the grey section at the bottom.
Then rename it, change the values and part no etc.
By having a common part you have to change the part no, values etc for each design and mistakes can easily be made.
outputting a part based BOM works very well when each value resitor/cap etc has it's own part.
Make sure the value, wattage, case etc are in the part name to aid selection.
I.E. SMres33k1%0402
By using SMres you can seperate it from a PTH one (PTHres)
Depending upon your MCAD system spaces in the name may not be a good idea for IDF output.
Value, tolerance, case etc - having all these in the part name make selection easy.
Putting them in different folders within the part manager hierarchy also helps.
I.E. all 0402 in one, all 0603 in another etc.