I suspect the reality is a little more detailed than you describe. There are a lot of details missing that could make a big difference in the approach.
Generally the best practice is to identify the objects (check boxes, buttons, etc.) you want to click on, rather than click at specific x,y coordinates. Things move around on the screen - Windows might be in different places, scroll bars might be at different points, even the content in the window may change. Targeting the object, though, depends on the application in question.
If it's a web page the best idea is to examine the page's HTML and craft a JavaScript to do the work - that's one of the core competencies of JavaScript. If it's not a web page then you should look at the application in question and check its dictionary for what AppleScript support it has. Failing that, fall back to UI scripting, with all the caveats associated with that.
At its lowest level, this will do literally what you ask, but I maintain there is a better way of doing it:
set loc1 to {500, 600} -- x, y coordinates
set loc2 to {1200, 90}
repeat 1000000 times -- that's 'multiple times', right? :)
tell application "System Events"
click at loc1
delay 0.5
click at loc2
end tell
end repeat
