If I have a pitcher with 5 pitches and his ratings for each pitch are as follows:
Pitch 1 - 80
Pitch 2 - 70
Pitch 3 - 35
Pitch 4 - 75
Pitch 5 - 40

Does he still throw his #3 pitch more often than his #4?  I've been given a spreadsheet that I'm tweaknig that's hopefully going to help me do better in the amatuer draft and I'm curious as to how much weight I put on each pitch.

I would assume that the better pitches will be called more (and this may be dependent upon the catcher).

Anyone have any thoughts?

individual pitches are not thrown.

You can google for more of this interview:

To simulate a plate appearance, we break it down into steps where if one result is achieved we advance to a different step than if another result is found; like a "choose your own adventure". Assuming a normal game situation with no one on base, we look at the batter's walks per PA and the pitcher's walks per batter faced to determine the likelihood of a walk. A random number is drawn. If it is within the constraints of the probability, a walk occurs. We do the same with hit by pitch.

If neither occurs, we move on to whether there is a hit or an out. Ballpark factors, lefty vs. righty splits and specific weighting from extreme hitters and pitchers comes in to play here, but essentially this is the hitter's batting average compared to the pitcher's average allowed.

Somewhere, sitestaff said that the pitches are used as a weighted average, with the best pitches, not the first pitches, weighted most heavily.  So P4 figures more heavily into the sim equation than P3 in this case.

So if I'm looking at writing some code to help me with my draft, I should probably weigh each pitch the same, instead of weighing pitches 1 and 2 heavier than pitches 4 and 5... right?

For the most part, order of the pitches doesn't matter.  The only importance of order is that the first pitch is the "out" pitch.