Hungriee..any pics we can see? As far as the plants, that's cool they're breaking the water surface, some do. My pennywort BK828 sold me does just that. But, to answer your question, yeah, right now I use my hands, cause I don't have tools yet. I know when you trim, it gets everywhere, but that's just what can happen. Patience and taking your time will help. Also, I do use a fish net to take out some of the left over pieces. Anytime your skin is not in the water is a good thing. I know some peeps here would say human skin should never touch the water. Even the slightest bit effects the tank. But, I'm just beginning, and soon, prolly will graduate to trimming tools.
I do replant my plants bank into the substrate. I use eco as well. I need to trim my rotala and baby tears this weekend. If it gets cloudy, just give it a few hours. What kind of filter are you running? Try to move slow and disturb as little as possible. It takes patience and care, but that is the life of an aquascaper. Hope this helps.