If i have an account, that has 1 main and 2 alts what are my options to assigning DKP to that player. and how does the website / GRSS MOD know who is linked with whom.

I believe for some of it you have to know who is who from alt to main. When you upload a raid from GRSS to the site you should a "played by" drop down next to every name. Here you can change it from an alt to a main to award DKP. If memory serves me correctly Chops made this work such that it remembers the changes you make as an association.

Ok sounds good... 1 question with this, When an alt is in the raid, and an item drops, you type /GRSS SHOW will his alt be on the list with 0 DKP, or will his main be on the list with the current DKP amount

The character with the DKP will appear on the list. The alt will not appear on the list unless the DKP has been assigned to him.

This request also has the following ticket: http://www.dkpsystem.com/viewthread.php?threadid=5018

Show it your support for faster development.

And of course this is when you select the "Guild" option in the dropdown list, cause if you select "Raid" then it will only show those members in the raid ?

Yes!