Geckoes are not really good for paludariums. They do need humid enclosures, but not watery ones. Some could eat your fish, yet it is rare. For a paludarium I would instead get anoles, for their small size. They give you less trouble with land areas as they can pose on some plants without breaking them or falling down.
As for the water/land thing, for frogs and newts I find much better to use a large piece of bogwood rather than glass/acrylic dividers, or false bottoms. Do just a half full planted aquarium with large wood pieces coming out of water, enough to give room to bask, and tall enough to be able to dry.
For plants, with adequate light, about any you like. Swords do very good emersed, and give a dense vegetation marshy look to the surface. Nymphaeas and other lilly-like leaved plants look and do fine too. Avoid hornwort, cabombas and those which lose a lot of leaves and make water a mess, frogs are less gentle with plants than fish. However, the substrate choice will depend greatly on the kind and size of frogs you want to have. A layered one will be more susceptible to mess up if digged or disturbed too much. Bear that in mind.
Filtration will depend on how many plants and animals you have. Inside power filters are the most used in this kind of setups, and they can be hidden fairly easily.
Other animals? Well, newts and frogs are already regarded. I guess the usual critter buffette: shrimps, snails, clams. Even a small creek snake could be put in. With the bogwood layout I suggested, archer fishes would look great, however they do better in brackish water.
Look around, read much, and look at as mcuh pictures as you can to find out what you want.