In any case I was having a huge issue keeping the work relatively flat. No matter how hard I tried the planer would be at some sort of angle and cut into wood on one side more that the other (usually the side opposite of me. ).
It sounds to me like this may be due to a combination of factors, the first is just one of technique, something that will improve with practice and experience. Hand-held planers are powerful, like belt sanders, and just like them they can run away from you if not held right. That might be better expressed as they will run away from you if not held right!
You may have been trying to take off too much on each pass which would be a critical factor if that's the case. Even at a low speed the bite into the wood will make control difficult. Unlike a belt sander, with a planer you can control the projection of the blades and because they're so effective having them set to remove the smallest amount possible (equivalent to 0.1mm?) will make it most controllable.
In terms of technique I think you should be trying to have the planer 'take off' at the end of each pass, like a plane lifting off from the end of a runway. This is even good practice with a hand plane, and I seem to recall when watching experienced users wielding planers that they do this at each stroke. It contributes to the fatigue of using them as you're lifting with arms extended, but that can't be helped.... probably a good reason they shouldn't be used heavily by the amateur woodworker.
One other thing, it's not clear if you were planing along the boards or across (not just at 90°, even at an angle) and this may also be a factor. If you were planing across that will account for some of the difficulty I'm sure. Cross-grain planing is much easier that planing along the grain, something noticeable even with a hand plane.
It might not be the right tool for the job but it is what was available.
The right tool is often the one that's available :-)
But this may be a good illustration of why planers aren't the ideal tool for smoothing larger surfaces. They're great at removing wood quickly, especially from edges narrower than the cutter head, but they shouldn't be expected to produce a good flat, smooth-ish surface as if you'd dressed the board with a jack plane.
Mentioning the jack just above brings to mind another thing, if you were cross-grain planing it should be expected that the surface isn't great after that step. When flattening a board by hand all cross-grain work, whether by scrub plane or jack plane, is further flattened out by planing along the grain afterwards.
It's only that last step that produces a decently flat surface, which is then taken closer to finished with a try or jointer plane before final smoothing.
In your situation this planing along the grain to flatten off should be done by handing off to your thicknesser as you did, so within reason you should expect the board to look rough before it goes into the thicknesser, which will combine jointing and smoothing operations in one.