I believe that if you are using RobA's tapered stroke path script it will only do one path at a time. So each river, even each branch has to be done separately. One thing you might take a look at is which path is selected in the paths dialog. You should be able to do as many paths as you want in one layer and then run the script on each one. I just ended up using the ink tool with little to no flow settings and started at 1 and went to 3.5 px or so in 0.5 px gradations to the sea. My map is here for reference.