I run with my dogs on a lead. One at a time, and in different circumstances.
Max, a Weim, is very skittish, and gets a bit hyper when he's around cyclists, other dogs, crowds etc. So he and I do my solo long Sunday runs on quiet roads. I keep him on a lead, yes he usually needs to go at some point, I'll always carry poo bags, and then spend the next 10 minutes looking for a bin!
Mini is a cocker spaniel, and much better with groups of people. She comes with me on park runs. I use a chest harness and a short lead to make sure she doesnt get under people's feet. I try to ensure she's peed and pooed before we start, but occasionally we have to make an unscheduled stop. I run alongside the grass where possible.
It's a matter of getting them used to it gradually, and recognising what is going to work for each dog. Serious Canicross folk use a waist belt to attach the dog to, keeps the arms free.
Oh, and no running before a pup is 12 months old, as their bones arent fully formed.