1.) When uploading a snapshot, the website considers single boss fight its own unique raid. I understand that some people don't stay for an entire Naxxramas so then it could base attendence off those who stick it out for the duration of a raid. If this isn't the case, is there way I can upload a Naxx raid and it not break it down per boss fight?
Just tie the uploaded snapshots to a calendar event. The term "Raid" is going to be replaced by the term "Raid Snapshot" or just "Snapshot" to remove the ambiguity associated with calling a single snapshot a "raid". Tying all the snapshots to a calendar event will remove that particular issue. There's almost no reason you would want to remove the granularity of having each individual boss there.
2.) Item- values. Is there a way I can load a raid and to have all values already entered? If you take a full clear heroic Naxx raid over 15 bosses- 4 drops per boss that would mean 60 items that need customization. That's ALOT of legwork.
Currently, no. That's a feature that I'm working on to allow guilds to auto-populate item prices based on stats.
3.) Am I understanding this right? If I run the getGRSS.exe file before I even start the game at the beginning of a gaming session, the mod will upload the already stored data from my site into the mod/ game so when it starts I have current (at least what is already posted on site) data availability for that nights raid?
Correct. Run GetGRSSDKP.exe before each raid and the mod will download the current standings from your site as of that moment, and import them into the game.
*Suggestion* Having people's rank/ place/ points appear in their officer notes for quick reference on the fly.
Keep in mind, in a raid, users can just send you a tell with !dkp and it'll give them their current DKP. If neither you, nor someone who runs the GRSS mod is online, the website is just a Alt+Tab away