Scooter blennys belong to the same family as green and spotted mandarins. Their mouths are specialized to the type of food they most commonly find in the wild; that is, the small microcrustateans, worms, and copepods found on the rocks and sandbed. It's a shame that they are sold so commonly as "beginner" fish, but they are pretty much ubiquitous to any LFS and even chain fish store you walk into.
The good news is this: of all the Synchiropus genus we see commonly sold, the scooter blenny is the most adaptable to normal aquarium food. They definitely need the microfauna of a fairly established tank, but they will survive on frozen mysis if need be. Think of the mysis as a stopgap measure and you will be doing well: feed enriched frozen mysis, preferably soaked in Selcon, while seeding your tank with a few bags of copepods. I'm afraid your LFS guy misled you when he said they'll eat rotifers.....that's reserved more for the young fish, not an adult scooter. That type of food is a little too small for most adults.
If you're still having trouble getting the blennys to eat, try live adult brine shrimp. Most LFS's sell them. You can enrich the brine by adding some live marine phytoplankton to the shrimp's water for a few hours, and perhaps some Selcon vitamins as well. Brine shrimp are like candy to most of our fish -- it's a good food to get their feeding response going, but they have little to no nutritional value. The shrimp are filter feeders, so soaking them in phyto and selcon will gutload them to provide a little more nutrition for the fish. After the brine have soaked in the phyto, spot feed the blennies with a pipette to make sure they get it. After a few days of live brine, you ought to be able to wean them onto the frozen mysis shrimp.
As for your pods, you only need a couple bags to start seeding. If you're worried about the filter, don't stress too much. Are you running a sump style or HOB filter? If you have a sump, do you have a refugium section in it? The fuge is a perfect breeding ground for pods: get some chaeto algae in there, add a bag of pods to the fuge. The pods are so small that they will be swept through the return pump's impeller and into the main tank undamaged. You can also add a bag of pods to the main tank as well. Best bet is to turn off the return pump, float both bags for a few minutes (even pods should be mini-acclimated), add a little tank water to the pod bag, float for a little more, then add the bags. With the pumps off, you ensure that the pods will get down to the rocks of your display tank and into the chaeto of your fuge. After a few minutes you can turn the return pump back on and restart the overflow. Some pods WILL die in the filter floss (or sock, or whatever) but you'll still have enough to get a breeding population going.
