Using create water at the end, means that your erosion devices won’t drain realistically using it. But then using it in the beginning means heavy shape changes will destroy your river.
The best method I’ve found so far, is to separate the part where you create your terrain “shape” and primary geology. Do this part first. Then afterwards, try not to reshape the terrain too drastically. For example, no coast erosion. Use it before as suggested by @HYLK.
Then for just good rivers, plug this terrain into “flow restructure”, then create water. Trick is, don’t let your rivers “climb” the terrain too much, becomes tougher to manage the higher they get.
Then you can erode the terrain to your heart’s content, plug in the water systems so eroded terrain drains properly.