I'm honestly not sure what part you're talking about now. The game, as far as I know, should only display on the top screen.
Well, like I said before, once you select your cheats and start the game, you cannot return to the menu to pick different cheats without resetting the game somehow.
I'll write up a description/tutorial on what you'll see and how the menus work...
Assuming you have correctly patched and injected your GBA title, the following will happen after you launch it; If enabled with Luma (or comparative CFW), the game will load into the GBA boot screen. Afterward, the cheat menu should display. The first line of text will be the game's title.* Following that is the main body of the menu, the cheat list.** The cheat list can navigated by pressing Up or Down on the DPad, which moves the colored select bar. Putting the select bar over the name of a cheat on the list and pressing A will activate that cheat. You can tell which cheats are on by looking at the far-right column of text in the cheat menu. Cheats labeled "N" are deactivated, while cheats labeled "Y" are on. To deactivate a cheat, simply move the select bar onto the desired cheat name and press B. Finally, you can press Start to leave the cheat menu and begin the game. The scrolling text along the bottom details the same controls I've explained here.
*The title may not be there if you or the person creating the cheat patch failed to include a title in GBAATM. Some menus may also likewise feature customized font colors, select bar colors and backgrounds.
**Dunno how much extra detail people want, but the cheat menu is a scroll-able field of seven entries, with a maximum of 24 (25?) characters per line in the cheat name. I'm unsure how many entries in total the menu can have, I've never needed more than a dozen or so cheats for a game (a good idea is to pick only the cheats with the best utility, or that do the job of multiple cheats).