This sounds a silly question, but I couldn't find an answer to it anywhere. Once with Peyronies Disease, does it really matter the position of the penis inside the underwear? Should it be downward, upward, slanted left or right?

It does not matter at all. Totally up to your preference. Has no effect on penile health.

Both my uro and PCP said it doesn't matter, I asked the question of which is better boxer briefs or boxers since the briefs would keep everything snug.  

I have a small congenital curve to the left because I weared my penis on the left side of a boxer for all my life.

But correlation is not equal causation...

So I expect it could have an effect on the very very long term. I am using something loose ATM as NTE with daily Cialis are unpleasant in tight underwear.

Congenital means you were born this way. Which way you dress your penis does not have any effect on this.