The Boot Header {H1) on the board near Q9 is used to reprogram the CPU in MegaSquirt® (not the tuning parameters, but the actually code that uses the tuning parameters). It is NOT used for MegaSquirt-II. Leave it open, and do not jumper it in either case. In most cases you won't need to touch it. Depending on what you want from your MegaSquirt® EFI Controller, though, you may end up using the boot header to eventually to load customized code, such as MSnS-E, etc. To load new code, put a short piece of bent wire between the two H1 holes. Some people have put a momentary switch across the boot header, and place the switch so they can go into bootloader mode simply by pressing this switch while powering up, without opening the case. (If you do this, be sure it can't be pressed accidentally.) The instructions for loading new MegaSquirt® code (not MS-II) is here.
DO i have to do this in order to FLASH the computer its the DIY msI v3.0 board