That depends. I always take into account these two things first:

1. Can I take advantage of the extra refine points after I upgrade? If you have enough runes to keep going till you get to the point where you need advance refines for that equipment, then go for it. You must take advantage of the extra points you earn after every upgrade.

2. If you have 500 runes to spend in total, then definitely go for it and get all the rebate items.