First is how do we get our boss kills to count toward guild boss kills?
For tracking Boss Kills or raid achievements many guilds/servers also use WoW Heroes.
Do we need to have a full guild group for bosses to count or is it an overall percent of the group that needs to be guild members?
This is a two part question.
Part 1 - On the WoW Heroes site is a comprehensive set of requirements for a guild to be able to "Claim" a Boss Kill or Raid Clear. We have used their requirements (altered just a bit to suit our guild) to keep track of our guilds progress. (Such as 10 man raids, must consist of at least 7 guild members including 1 officer in order to be eligible for guild claim. 25 mans must consist of at least 16 18 guild members and include 2 officers. But, this came about over time as we are very casual about raiding.)
Part 2 - As for needing a full group, there are many achievements in the game at this time for Downing a Raid Boss with less than a full group, Example-Less IS More and many are fun to do. However, until they can be trying on a group new to the raid. I would suggest, taking a look through the achievement list and if your group is up for it, picking one to have a go at. If it doesn't work, never fear, you can still finish the raid normally, and be proud to have tried.
Do we have to self report (where?) or is it counted somewhere like armory/ wow heros where we can see our over all progression?
On the WoW Heroes website, you or an officer of your guild must report any raid progression yourselves. The site will check it against your wow armory achievements and update your rank in the server list.
As Xythan above said, please do not focus on progression, its a game of cat and mouse that is almost always frustrating. Watching your guild climb several ranks, only to drop several more can be disheartening to say the least. However, there is a sense of pride the first time you see your guilds name in a ranking system. Raid because you like playing with your friends and guild mates, Raid for fun, and for the loot and you cant go wrong.