I think you're asking the right questions, getting good answers and taking away the important information. Keep asking the questions and I think you'll be ready to stock your FOWLR
tank once your cycle is complete.
You're right not to run a skimmer during the cycle as it removes those ammonias you want to build up in the cycle. I would add the cocktail shrimp Todd mentioned for the cycle vice ammonia as it is easier (no chance of getting the wrong ammonia or over dosing) albiet less controlled. With the Fluval filter, you will need to ensure you clean it regularly as they can cause a build up of nitrates if you don't. But they do provide a nice place to run other medias for control of nitrates, phosphates and silicates. Again, not during the cycle.
If you're going to add more rocks as well, do it during the cycle. That way you don't have to cycle them in a seperate container.