Maybe I'm not following you correctly. Are you using a tablet? if so, the below is not pertinent.
I don't use a mouse either, but if you select your hexagon and left click on it again you will see the reg and curved rotation handles pop up, just grab a curved one and spin it til you have the flat bottom where you want it. Do that before you clone it. Not sure if this is helpful, but it sounded like not using a mouse could be the issue...