I am having trouble linking two people from different parts of the tree together as married. I half a daughter on one side and a half brother on the other, and I cannot link them together.
You will find that the graphical presentation of GenoPro is very flexible. You can select any element on the display (individuals, connecting lines) by clicking on them with the left mouse button and moving them on the screen. You can select more than one item either by holding down the shift button when left-clicking on additional items, or by holding down the left mouse button and dragging the mouse to select multiple items; the complete selection can then be moved together.
Select the two individuals (left click on the first then hold down the shift button and click on the second), and then either click on the 'Link as Mate / Link as Spouse' button on the Toolbar (see below) or hit Ctrl+M. A Union Line will be drawn between them.
By the way, there is a 'How To' section within the forum - this query would have been better listed in that section
You don't mention which version are you using, it might be helpful to make reply easier.
I beleive that you used AutoArrange function... It might be useful but just to some extent.
If all interpersonal connections are now visible and correct, I suggest that you use PartialAutoArange (available in recent beta versions) for families you want to have in groupes. (You have to select manually person by person (CTRL+RighClick), and all relationships among them.)
After that you should manually arrange horizontal and vertical distancies among families and individuals, multiple marriages/relationships and anything else you think that should be arranged...
If the tree just stays to complex, you might try creating a hyperlinks for individuals...
AutoArrange (nor full nor partial),at this time, is not THE tool to be used to arrange family tree, it just helps to get started or untangle confusion of family tree!
'Hope I helped!