If I switch my PG and SG in the starting line-up for def. reasons will it effect my turn over ratio? I mean, will my PG (really a SG) handle the ball more because I have him at the point or will my SG (a true PG) handle the ball more?

1) what are their relative position effectiveness ratings at the positions you wish to play them?

2) you can use your defensive match-up settings (second page of coach's office) to make the SG available to guard the PG spot while still playing SG

As long as the player is 100% at the position, the position does not matter.  (Magic is the same player at SF as PG)

As felonius states, you can use that page to adjust who each player guards.

The higher rated defensive player will guard the best defensive player that is checked.

"The higher rated defensive player will guard the best defensive player that is checked."

Did you mean will guard the best "offensive" player that is checked?
I used the match-up section, but I thought a starting PG would guard his position (i.e. PG) even if it was not checked. Wrong?

q1) yes he meant best offensive player - your highest rated defender available to guard the position willl cover his best offensive player
q2) only if you click on the 'only defend current offensive position' option otherwise the answer to q1 applies

also, a player will defend the position he started at whether you have it checked or not.  For example, if you started MJ at the 2 and Pippen at the 3, but you wanted Pippen to guard the 2 and MJ the 3, you would uncheck Pippen being eligible to guard the 3.  However, since he started at the 3, he will still defend that position anyway.  The only way to make someone avoid defending a certain position is to uncheck it and not start them at said position.  Not a big deal now, but before, Pippen wasn't 100% at SG for much of his career.

Or you could not listen to the guy with zero teams.  As long as a guy is 100% effective at the position, he'll play like his advanced stats indicate.  Sort of.