Ok, THIS is the bit that everyone is confused about, I think.

All DOOMS require a WAD, this contains all the game information, like sounds, graphics, level details etc. etc. If you don't want to pay for one, use the Shareware WAD from the original Shareware DOOM. This is availible at

  http://www.dtrance.ch/doom/download/Doom-[Shareware].lzx

and

  http://www.pluk.com/

I think. This is the ONLY WAD you can use without paying. If you want to use all the hundreds of custom WADS and 3rd party levels (say from ftp://ftp.cdrom.com/) you need the commercial WAD. This contains loads of more information that these custom 3rd party WADS don't contain but the game needs. You can get this WAD by buying the Doom game and copying it over to your Adoom/AmiDoom directory. You can then use them by doing "Adoom -file custom.wad" etc.

If you have an Ultimate Doom wad, name it doomu.wad

You are NOT paying for ADoom or AmiDoom, but for the commercial WAD. Sure, ID software gave the source away, but they still want money :-)) Its only about 9.99 UKP, so go and buy it... maybe it'll encourage ID to give us the source to more games :-)

When you add a custom.wad via -file, it replaces one or more of the levels. The level and episode should be given in the .txt file that belongs to the WAD. E2L3 would mean that the wad replaces Level 3 on episode 2. Therefore, to play that new level, you need to play the game until you get to level 3, after selecting episode 2. (The second one on the list....) OR you can jump to that section by typing in IDCLEV23. To jump to E1L3 it would be IDCLEV13, etc. Sometimes you might see E3M3, but it means the same thing, they just used the word mission, instead of level I guess :-)

Alternatively, you can warp straight to the level, by using the command line, 

 adoom -file whatever.wad -devparm -warp 2 5 -skill <skill number>

Where <skill number> is in the range 1 to 5.

Of cause, the easiest way is to tick the Warp option in DoomGATE, and then use the sliders to select the episode, then mission :-)