I have always preferred using affiliate networks as an affiliate. From a merchants perspective, I would think it would decrease the amount of work you would have to do as these affiliate networks already have a good amount of affiliates registered with them, plus they keep track of everything and take care of most of the fraud, if there's any.
Running your own affiliate program is not normally a one person job as it involves a lot of work and time to get it up and running. As mentioned above, affiliate networks take away some of the workload, but using an affiliate network is a little more costly than a standalone affiliate tracking software that you install on your own server, but in the long run it is most probably worth the extra costs.
Out of all the affiliate networks, as an affiliate I have always prefer ShareASale. Here is some more information about ShareASale
and some other affiliate software.
Good luck with your affiliate program and hope it all works out for you.