First, we need to find where the game is storing the custom level files. This is different on each version of windows, but they generally are in similar places.
A good generic way to find it is to search for %appdata%, with the % allowing you to search in hidden locations.
I have windows 8.1, and I could find my folder at C:\Users\COMPUTER NAME\AppData\Local\realbboy_Infiltrate
Now, go to the levels folder. You should see an example file, click on it.
EDIT: There currently seems to be some problems with the example file and folder showing up but everything will work fine if you create a \levels\ folder where I say it should be and make your own text files from scratch.
Now, in the 'levels' folder, make a folder with any name you want, this will be the name of the mod. Make sure to put this name in the 'modlist.txt' file in the folder ABOVE the 'levels' folder. If you do not have a 'modlist.txt' file run the game and leave the menu room, one should be generated. Put the name of your mod with the same capitalization in a single line of the 'modlist.txt' file, with no other mods on that line.
Here, you can see that each custom room is comprised of letters, 33 wide, and 25 tall. To create your own custom room, make a .txt file, name it whatever you want, plop it in a subfolder in the 'levels' folder, and replace the letters with your level design ideas using this key:
E = foespawn - places a random enemy, and has a 1/3 chance to place nothing
W = wall - A wall. Not much else to say
S = scamp - places a scamp
F = clannfear - places a clannfear
R = rug - 30% chance to spawn a rug
C = crate - places a crate
G = oblivion gate - places a gate, which is an exit
B = crate high chance - 15% chance to not place a crate
N = crate low chance - 10% chance to place a crate
P = player - only place one, or more than one if you want your game to break, hopefully in an amusing way
O = open - air, free space where nothing is placed.
NOTES: Make sure to leave open tiles on the edge of the map for the player to leave, and always place a player somewhere where they can reach an exit.
To get you started, here is the example level: (Note that the font that is currently being used isn't mono-spaced, copy this into notepad and it will look much, much better)