Avoiding stress
Yeah, don't worry about freaking your geckos out. Odds are you're going to be doing that anyway whenever you want to get them out to check on them or pick them up. I think lizards in general are always stressed out whenever they get picked up, and you will definately be doing that at some time or other in the future. I guess it is good that you're getting them used to that right now, before they get older and it really stresses them out from not being handled before. You should be handling them frequently after the first week or so, to help them get accustemed to you and to minimize the stress they will feel later on in their life, so stress is kinda inevitable in the beginning.
I have had my fire skink for nearly four months now and he still gets stressed out because I have to lift the lid to his terrarium, remove certain things in his terrarium like his log, his rocks and his hides, flush him out by slowly poking my finger into the Eco-earth, and attempt to pick him up without squeezing him or exerting any sort of pressure on him, all the while he's squirming like crazy. If that isn't what you would call stressful, I don't know what would be. And yet they tell you that you need to do this to get them accustomed to you :shock: ... :roll:
About the food dish, I think it would be good idea to get a clear glass bowl and try that because it helps me with my lizards. They can see the bugs moving around inside and my fire skink even makes it part of his daily routine now to check underneath the plant overlying his log where his food dish is because he remembers finding the bugs there in the first few days I had him. I think it will really help with your geckos. If it doesn't, you can always go back to your hamster dish. In the meantime, why don't you use the hamster disk to put your calcium dust in? Just an idea.