Ask any Grunt who ever went through Army Basic Training, or any Gyrene who ever went through Marine Corps Recruit Training - "comfortable" is not an adjective that is commonly applied to the LBE and ALICE pack. We used this gear because it was issued to us, and we wore it and marched, hiked, camped and crawled in the mud with it because we had to. Just because the military issued or used this gear does not mean that we would necessarily recommend it as a shining paragon of utility, durability or comfort. A more accurate description would probably be "not intolerably uncomfortable, most of the time." If you can't afford to spend a bunch of money on top-echelon gear, surplus LBE/ALICE is a decent value, but MUCH better gear is out there.
First, you put on your LBE - it helps if you get a friend to adjust the straps for you while the gear is on your body for the first time(the adjustment process goes about 3X faster with a friend). The 'US' on the yoke should sit right between your shoulder blades IIRC - you don't want the yoke to ride too high up on your neck, for comfort. Try not to have any kinks or ripples in the suspenders as they hang on your torso. The pistol belt should ride naturally on your hips, and should not be too tight. Once all the straps are adjusted properly for you, use electrical tape or duct tape to tape down the loose ends of the straps.
The ALICE pack goes on top of your LBE; again, you don't want the pack to ride too high on your shoulders, it'll wind up pressing down/forward on your neck, which will suck after marching a few miles. I personally found the aluminum pack-frame with the kidney pad to help a lot with pack comfort, but others said they preferred the pack without the frame. If you have a "butt-pack" on your LBE, it may cause the pack to ride too high for extended comfort.
Key words to remember with all things military surplus: "Supplied By The Lowest Bidder." This stuff is not issued because it is the absolute best, it just happens to be "mostly good enough" for the right price.