I prefer to do both the pillar and bedding at the same time. If you're installing new pillars, you're probably going to have to epoxy them in place, or at least use epoxy to mold the pillar to the stock, as you might when using factory style pillars from Stocky's. So to me, it's best to do all the bedding and pillar fitting at the same time.

How you do that, or the order you do it in, is totally dependent upon your own skills level and what tools you have available. I'd highly recommend using Devcon 10110 and a gram scale to weigh your batches. It's really important to get the batch ratio correct.