There is no shame in using mechjeb and when docking is released it may become even more handy. With mechjeb you can add a lot or a little amount of automation. But you still have to build the rocket to do the job.
As for your questions, they are tough to answer.
As for colliding with other debris, i have not done that yet. I have had loads of debris in orbit, but not come close. However as a general rule for me, i try to create a rocket where i dump parts back into the atmosphere so as to try to no "litter" orbit.
I feel your pain with fuel. But when you crack that magic combo, it will be worth it. Just remember it will all change again on 0.17 as there is a little exploit in game that most people use without knowing. That has already been rectified and will cause a need for change in your designs on the next release.
Just keep experimenting. Its like a mini puzzle game where you have all these different pieces and you can use any or all of them to complete the puzzle.
But yeah, its a brilliant game which is only getting better
Why do we love a country where everthing in it can kill us (even the women)