The first step you'd wanna do is to set up the palettes in ZC. You've already been building the tileset following NES rules, so that'll simplify it (ZC can handle 15 colors + transparency per tile, and that's not counting using 8-bit mode, but still, following NES pecs means you've got a ZC-compatible palette guaranteed). To do that, you'd wanna go to Quest->Graphics->Palettes->Levels, find a blank palette (or just overwrite the first one), and rip your colors in. Csets 2-4 are the csets used for overworld/dungeon/environment colors, so for each, you'd have color 0 be transparent, then colors 1-3 be the three colors.
With that done, you'd go to Quest->Graphics->Tiles. Find an empty page or delete tiles to make room. Click the grab button, then click file, and select the image of your tileset. Likely, the colors will look wrong, but if you press R, ZC will auto recolor them into the current cset. This will allow you to select the tiles and rip them into the tile page. Selecting the upper left tile, holding shift, and selecting the bottom right will let you grab a whole chunk of tiles at once.
Lastly, you'll need to turn them into combos. The easiest way to mass convert tiles into combos is to select a group of combos (selecting the upper left tile, holding shift, and selecting the bottom right), press M, then select a blank spot on the combo page. Each tile will be made into a combo, and it will let you set the properties of all the new combos at once (very useful if you're creating combos for a whole chunk of solid objects and only want to set solidity once). Keep in mind that the combo page is only 4 combos wide, so if you select a chunk of tiles greater than 4 wide, the result will be a little funky looking.
I hope this helps. I tried to make it as newby friendly as possible, though I admit a lot of ZC isn't the most intuitive to newcomers, so if you need any help (for example, what a cset is), happy to elaborate.