I also had loads of trouble figuring out how to play, but finally beat the game :)
For anyone else wondering - you have to first place the portals with RMB by aiming them at the gray walls, only after you have 2 portals you can start pushing the ball with LMB. There are always 2 portals of the same color - one is shrinking you down, one is making you bigger, depends which one you enter. Enjoy!