Sounds to me like you aren't pulling correctly which may stem from a setup problem. The trapbar is going to move the resistence to the center of your body. Obviously just thinking basic physics this is going to make it significantly less of a pulling movement since you are no longer pulling back on the weight. This is going to favor people who like to shift the emphasis off the posterior chain away from the hams, lower back, etc. I don't view this as an equivalent substitution that simply works better for certain body types - there is a sacrifice here and IMO you had best learn to pull properly and once you've covered the fundementals experiment with this to see how you like the results over a training cycle (just because it feels easier is not a good reason to use it and neglect fundemental pulling nor does it indicate that your results will be better over a period).
If you are going around your knees, you need to start with your back flatter relative to the floor and butt higher. This will allow the bar to move up the legs and clear the knees naturally. I get the feeling you are squatted down fairly low with an upright torso and your knees sticking out - shoulders significantly behind the bar. Try experimenting with a position where your shoulders are directly over the bar that might help you get a feel for where you should be. If you can post pictures of your starting and midpoint position it would be very helpful (video even better). It's incredibly hard to diagnose on a text forum. Incidentally if this upright torso, deep squat sounds like your starting position, it's indicative of relative core/posterior chain weakness (in general but not every case but I'd lean heavily this way) which makes it even less acceptable to avoid using a standard deadlift.
EDIT: Also, aren't you in mid training cycle right now? I'd be really hesitant to swap out a lift unless absolutely necessary. Better to put some time into learning to do it right. Also, you know not to touch and go on your work sets - each rep is a pull from a complete deweight upon the floor. Meaning, let that bar settle on the ground, reset slightly if need be, and then repull the bar for the next rep from the floor.
EDIT2: As long as we're on the subject of the trap bar - I also don't think it works optimally for developing the traps either. The function of the traps is to pull up and back. This is why olympic lifts and variants like the power shrug are so damn good at building them. With the weight centered relative to one's body, you can't effectively pull back. On top of that, the traps and upper back in general respond to dynamic lifting like it was their sole purpose in life. As a builder of traps this thing is pretty far down the list.
