I am not quite following.
So you want to use emulator substitution methods (if you see this graphic rather than display the sprite in the game display this PNG instead) to make NES games look fancy.
You went and looked at an emulator that has such a feature, in this case mesen, but found it rather complicated and unpleasant to use.
You instead found a level editor whatever for the games but it had a nice UI you could deal with.
You then want something like the UI of a ROM hacking level editor but to use for the graphics replacement options of Mesen.
I had missed this becoming a thing on the NES. Normally we see it more for the N64 and PS1 and have the earlier stuff just use increasingly fancy and game specific filters. That said the principle is fine in theory.
The reason the hacking tools you might have grabbed on a site like this are nice to use is because someone/a group possibly spent thousands of hours decoding the game, noting where everything what, what everything did and building a tool to handle it. The emulator will lack this and instead either dump things it sees during its play time or just reads the ROM which is built to run a game, not look nice for someone to edit. The graphics replacement then being a glorified "if you see this then display this instead".
If it is just for a game that is well known to hackers (Super Mario, various Final Fantasy games, Megaman, Kirby, Metroid and a few others) then between the emulators, stuff on https://datacrystal.romhacking.net/wiki/Category:NES_games
and whatever disassemblies there are for games they could probably do some things.
If you are not a hacker and not willing to learn then you can possibly still get something done, but will not gain anywhere near as much as someone that knows what they are doing.
You might be able to use graphics editors to learn the locations of things you want (assuming it does not outright tell you where it is looking then if you edit it then what changed in the ROM will be where you need to point the replacement things in Mesen at) and the various ROM and RAM maps on the wiki above to learn the locations of things, you might even be able to use some basic tools to learn some more for yourself. Disassembly listings without knowing at least some basic programming concepts will not do much for you, if you do know some assembly you can find out where things are remarkably quickly compared to the other methods assembly is one of the harder aspects of programming things.