After you've saved the DS9.ini file and started up the game, the map that you replaced title.dsm with will automatically load, bypassing the main menu. Once the level is loaded, all you have to do is hit ESC to access the main menu again.
Add (Virtual) Infinite Health
During the game, press TAB and type
"SET PLYR.DS9_[character name here] HEALTH 999"
When I say [character name here], you must put in either SISKO, SISKOEVA (if he is wearing a spacesuit), KIRA, KIRAEVA (if she is wearing a spacesuit), KIRACARD (you'll know when to use this late in the game), WORF, or WORFEVA (if he is wearing a spacesuit). The actual number "9999" can be any positive number up to 9999999999 or so.
Increase Jump Height
During the game, press TAB and type
"set plyr.ds9_siskoeva jumpz 1000"
OR
"set plyr.ds9_sisko jumpz 1000"
depending on which level you are on. This cheat code varies depending on the level being played (sometimes the "eva" suffix is required, sometimes it isn't), but if you try them both, one is sure to work on any given level.
One final note on Health/Jump increase cheats: they are dependant on which character you are using. The above assumes you are using Sisko but if you are using Kira or Worf you must replace "sisko" with "kira" or "worf" in the "set plyr.ds9_sisko" line.
Long Lasting Energy Beacon
Hit TAB and type "set plyr.ds9_flashlight charge 9999".
Quick Exit
Hit TAB and type EXIT = this will quickly quit the game, bypassing the main menu, and take you back to Windows.
Quick Savegame
Hit TAB and type SAVEGAME = this will save your game without having to go through the main menu.