I haven't used assemblers, so someone more experienced can answer the actual question.
What do you exactly mean by "implementing through fceux"? I understand it is mostly for running the ROM while allowing us to view the content of RAM and ROM and the registers.
If you know the asm code you want to turn into assembly, you can do it manually. I assume people use tools when doing it a lot, but it might help understanding at this point (if there is not a great amount of it). You could post your asm code here if you want? It basically means mapping the asm to opcodes (machine language). 2 byte addresses go in reversed order (little-endian). A helpful reference for a beginner (or any 6502 asm coder) would be: http://www.obelisk.demon.co.uk/6502/reference.html
(some of the other pages are definitely helpful as well http://www.obelisk.demon.co.uk/6502/
, NOT much to read)
If you want to change existing code, you want to replace some bytes in the ROM with your bytes (=opcode sequence). This can be done in a hex editor. You need to figure out what the location is in the ROM. This depends on whether banks are used or not (mapper) and the banking mechanism, if used. I guess the easiest way is to search for the existing bytes, they should identify it quite well. If the amount of new bytes is less than that of the existing bytes, there is no problem, just return earlier or add NOPs or jump over. Otherwise you need to find free space (from the same bank if possible) and do a jump to it, and possibly jump back, depending on if it is a called routine or something else.
Did I forget anything?
Oh, everything may be game specific, as far as the stuff you actually write is concerned. e.g. there is no "RLE", there are only various variations of it. Haven't checked what dte is, but it might apply there too. Also, even if you know what you are doing, it can be ridiculously easy to code bugs when using asm. Though that is kind of irrelevant until it happens.