I had lots of fun trying to manually setup maximiser until I started using keyclone. I confess I just put in numbers and looked to see what happened

For 2 windows it depends on your setup, if you have 2 windows on one reasonable size screen I'd actually recommend not bothering with maximiser, open up two windows get them to a comfortable size and have them overlapping so by clicking on a window you bring it to the front. has the disadvantage of not being able to see what is going on in both windows but does mean you can be comfortable with the window you can see. if you have a large screen then go fancy

If you want to use maximiser then keyclone does it brilliantly. you can drag boxes to the size you want in the setup window. the biggest problem i had with keyclone is getting the mouse to let go of the box when i resize it but clicking enough times worked. you will also see a box showing the dimensions of the window box so you can fine tune your numbers there. Keyclone does a good guide and explains things way better than i could Keyclone also does a good job of adjusting the picture resolution to the box size you want so the game won't look too weird

Hope that helps