Hello, Luis! Welcome to the site. I started off with no spacers whatsoever and thought that looked just fine. Looking back now, I shudder to think what stresses I was subjecting various parts to assembling things that way, but I mention it here just to point out the fact that it is very possible to get these spacers wrong or to leave them out altogether and have it seem to be "right" when in fact it is definitely not. Schwany's thread on his P11 was a huge help to me in determining where the spacers are supposed to go; go through my thread you'll also find other helpful links, including references to a list which details the thicknesses of specific spacers, which was good info for me as I ended up making all my own new spacers on a lathe. But to answer your specific question:
At two or three points along the way I thought I understood the spacers; I was wrong every time but the last time. Page 8 of this thread is where it finally all comes together properly. I think the best way I can describe it is that the engine needs to go to the left and the transmission needs to go to the right. Earlier I thought that all the spacers needed to go one one side, and indeed it will fit like that, but if you do that then your primary drive sprockets won't line up. Pay attention to the front upper mount, it has spacers on both sides. Along the way it was helpful to me to remember that the frame was originally intended for a different engine and the P11 spacers are sort of an "adapter kit" to make the Atlas engine fit. Coming from Japanese motorcycles, this was a surprisingly difficult concept to wrap my head around--the Japanese don't do this sort of thing. If Honda had wanted to build a CR500 with CBR600 engine in it, they would have just designed and built a whole new frame to marry the CR500 brakes/suspension/bodywork to the CBR engine and would have done so apparently with casual abandon.
Remember that there is no need to force your engine mounting plates (do not assume that they must be under bending tension to fit properly--I wondered about that at one point, thinking to myself, "Maybe that's just the way the Brits did things?") and and also that things properly installed will be parallel and square. Holes will line up, bolts will be long enough, etc.
I'm happy to answer questions you may have, just be aware that I am currently on the other side of the planet from my P11--I work in Papua New Guinea and my P11 is in storage in the US right now and will be there for at least the next couple of years, so I can't just run out to the garage and take measurements for you.
