I'm using a program called iRed (with an IR transceiver) to teach discrete IR codes to my MX500, but I am a little confused.

For example the POWER toggle code for my Samsung HLP TV is "S111000001110000001000000101111110". (This is what the iRed program editor shows as the code.) The list of discrete codes for this TV (from the Samsung website) says the discrete Power ON code is '99'. Is the '99' code appended to the end of the longer code, or replace certain digits?

The code almost certainly contains more data than just the '99' which is the customizable portion (the part of the code that distinguishes one function 'PLAY' for example from say 'MENU'). Judging by the length of the binary code, you will have a really difficult time determining which part needs to be changed (and remember that you will have to insert the BINARY conversion of 99 into the right spot in the sequence REPLACING the code for 'power').

In any event, that kind of parsing of infrared sequences is well beyond my knowledge...I would just find the discrete ON and OFF in the files section of this site and download and import it (or learn it from another device) but I know there are those out there that can 'create' discrete ON's and OFF's given the structure of the code and the data for each function.