I really think you're experiencing some problems that are not inherent to the game, but to your specific installation.
1)Prestige points are awarded for destroying enemy units and taking objectives.
They allow you to purchase new units, during or beween battles or upgrade existing ones.
The percentage, obviously, determines how much of those you and the enemy gain per untit destroyed, objective taken.
It may affect purchasing cost also not sure.
2)Experience is calculated for individual units, it carries over from one scenario to the next in a campaign game, the percentage determines how quickly yours and enemy units gain experience.
It allows you to nurture crack units who become very powerful late-game.
3)"Hiden units" lets you play with F(og) O(f) W(ar), enemy units have to be spotted by your own to become visible, unchecked they are always visible.
4)Victory locations have small national flags in the tactical map, green or white hexes in the strategic view.
Airfields, in my version at least, are hexes with an airfield-picture, two white runways, a couple of hangars and three small plains.
I seem to have version 1.0 btw, don't know if that may be the issue.
Hope this helps