I know I'm still pretty new to HBD, so there may be a way to do this I don't know about, but it seems like you should be able to re-order the draft prospects by individual positions. 

For instance, Player A shows up as #23 overall prospect, and top first basemen. Player B is #29 overall and second first basemen. 

If you value Player B more than Player A and therefore want to make him the top first basemen, you have to manually move him to #23, but that offsets all the other rankings. There should be some way where you could simply switch Players A and B, making B #23 and A #29 while keeping the rest of your rankings unchanged. 

You can.  Go to Rank Players.   Move Player B behind #22 and Player A behind #28.

I know I can do it manually, I was just wondering of programming it so that it would swap them automatically, rather than putting B into the #23 spot and then manually moving Player B to the #29 spot

How do you define that logic in programming?

Yeah, I think you're asking for some Jedi mind-trick or something. 

Most likely I am...but that's the way I organize my draft prospects, and I like to be as detailed as possible so I try and do it for the Top 500. Organizing and analyzing 500 guys takes way longer than I have and I would rather spend my time analyzing rather than organizing, but I can suck it up if there isn't said shortcut

bruinsfan911 - I think you'll find you get faster and dealing with the draft the longer you play.  It's rare that there are 100 players worth ranking. After that they're all career MinL filler.  All that matters even a little is balance, so you don't end up drafting 5 1Bs and no Ps.

true. doing the top 100 manually wouldn't be too bad either. Thanks for the help guys

I can usually quickly identify the top 40-50 guys worth ranking.  No need to look beyond that.

Build a winner, "punt" the draft, and only target IFA! That way you wont have to worry about ranking players.