Yes, if your opponent is in front of you and jumps to your backside, you have to hold forward, which then becomes your new backside after you block the cross up. Hopefully that didn't confuse you. As for you getting hit, it will only be a cross up if they actually go over you. There are exceptions though, stuff like the shoto jumping LK is pretty ambiguous and can hit from the front while the character still falls behind his opponent. There are also unblockables, fake cross ups, and cross ups that don't hit as a cross up to worry about. But you probably won't find yourself in those scenarios too often so it's not something you should be too concerned about right now if you're still learning.
ah, I'll just keep practicing it then.
One big question that I've always had and that has always alluded me is the application of combos in a game. Doing combos in the lab is never a problem for me,(Ive even got the FADC to ultra combo on my weaker right side down now for the most part) but doing them in a game is a compeltly different story as I can never put myself or my opponent in a situation where I can hit confirm into a combo as I'm never in a close enough range to do so. The only one I can do is Ryu's option select of cr medium kick to haduken, and thats simply because it's an option select and the range of the cr med kick is pretty far so I don't have to be right up in my opponents face like 95% of Ryu's(or anyones) combos.