epicrean,
well first thing to know is what platform are you running AM on? Windows? Or a flavor of Linux?
Second, is can you locate your attract.cfg file? If so open it in an editor and copy/paste the content here for us to look at it.
Here's a basic example of a Display that you can find in attract.cfg:
display Arcade
layout nevato
romlist mame
in_cycle yes
in_menu yes
filter All
filter "No Clones"
rule CloneOf not_equals .*
filter Favourites
rule Favourite equals 1
your layout maybe different, nevato is just my favorite.
Notice how I have different filters all in the same display? By default a display will go to the first filter which is "All"
In AM press TAB and go to "Controls", scroll down a bit until you see "Previous Filter" and "Next Filter" for each, assign a key. to each. I used R and F simply because it mapped to my second joystick but you can use anything.
Now press ESC to go back to the main AM screen, and press the key you assign to the next filter and it should filter only the roms with are not clones.