beween custom game and custom scenario?

Custom only means that before the regular game starts you can make a couple of extra choices in the beginning like number of opponents, which opponents you will have, what victory conditions are enabled etc.
The difference is that when you choose "custom game" you play a regular game of cIV, whereas if you choose "custom scenario" you will play a mod or scenario which usually has somewhat different goals/victory conditions/maps/units/etc .