ok im installing a boost controller from diyautotune but im getting confused on how to build it. if i could get a picture of the boost controller diodes on a ms II v3 main board that would be great just need something i can build off of.

 

I assume you've checked the documentation?

MS2-Extra Hardware Manual

 

so i just put it in the proto area im just not understanding do i soldier them to each other or do i soldier them into the board. sorry im a *** with ms system and bout mine off the forum here so not to sure what im looking at

 

You solder each component onto the pads of the prototype area, and then connect each component using bits of wire, component lead, and solder.

This explains it a little, with pictures:
How To Megasquirt Your 2nd Gen RX-7: Building and/or Modding The Megasquirt