If you use FIFO, system will calculate FIFO method by combination Item+Variant.
If you use Average, system calculate depend of setup in Average Cost Calc. Type on Inventory Setup. You can choose next variants:
-by Item
-by Item & Location & Variant
If you want to use variants, you always need to use variants in all posting type. Also, if you use Sales Price, you must enter price for every combination Item+Variant.