You can use multiple loops, but I don't think that is what you need in this case.
As Jerico2day pointed out, everything is done in sequence, you simply can't do more than one thing at the same time.
But it all happens so fast that the user would never know this.
Here's the general layout that I use.
// The setup function is called once at the start of the program so is outside the main loop/
setup()
// The next bit runs in a loop for the duration of the program
do
check_inputs()
move_player()
update_level()
sync()
loop
// The rest of the program is the functions, these are called from the main loop as and when needed.
function check_inputs()
// Check pointer, joystick, mouse or whatever here
endfunction
function move_player()
// Move the player here
endfunction
function update_level()
// Update Level, scores etc.
endfunction
function setup()
// Do set up stuff that needs doing once like dim statements
endfunction
This is a very simple example, but it should give you an idea.
Think of each function as a task to be performed. As long as you call each one in the main loop, everything will be fine.
Each function does it's job and when it gets to the "endfunction" instruction, it returns to where it was called in the main loop.
At the end of the loop when the sync() is called, all the changes for that loop are updated to the screen and this is what the user sees.
In most cases, multi-tasking is an illusion. Not just with AppGameKit, but with computers in general.