Unless said weapon is cold iron or some other such rare metal (but especially cold iron!), it's cost of weapon+300 gp to make it masterwork+2000 gp to make it magic. Adding anything else to it, such as "Seeking" or "Flame Burst" you simply take the current modifier on said weapon, which in many cases is just +1, and subtract that amount (that is, the 2000 for +1) from the cost of the new enchantment (so adding Seeking to your longbow would increase it's cost by an additional 6000 gp, that is to say your longbow's effective +lvl is +2, and therefore costs 8000 gp + 300 gp + cost of weapon, even though it is technically a +1.) I'd explain it better in person but...
Thank you everyone.
No problem. I had similar issues when I started playing D&D 3e back in the day...