As I indicated before the currents in the Duro can be quite strong, so going upstream means that you will cover a shorter part of the river, than going downstreams, at least in the same time. In the last case you would have to go by train or bus to the starting point. I never took one of these trips, so can not advise you. I just took the 3-bridges tour. There are a number of companies, which run these tours. They are all close to each other and I don't think there is much difference between them. Just choose the one that leaves at a time that suits you and also look at the boat. Some may be more appealing to you than others. If you would have to wait a while is no problem, because there are many terraces around the area to have a beer or a coffee.