The longterm dps is averaged out in both cases. So for example 20% crit for 230% dmg and 80% hit for 100% damage is turned into a flat 126% modifier. Generally the light yellow cells can be modified manually while orange cells contain formulas and should NOT be altered. For BM, Beastial Wrath and Yeast Within are also averaged out over their duration assuming the hunter pops it every time it's up. Pet attack speed includes averaged frenzy. FI is also averaged. I did NOT however calculate focus-based pet abilities, but since both builds have GFTT those abilities should be quite spammable and their dps contribution should be comparable. So basically this math shows that while BM is slightly more mana efficient, it is also slightly behind MM in the damage department. Increased pet and hunter attack speeds and FI/BW are not enough to make up for the huge AP loss of about 400 (in my case at least), RWS, and improved multi shot damage. Although FI is slightly more beneficial for the hunter's group than TSA :/
Some stats are not yet used in the calculations even though they appear on the spreadsheet, such as mana value of water, amount of intellect etc. The idea is to set your current stats as they appear on your paper doll in the top part of the spreadsheet and then put in whatever stat bonuses/penalties you want in the Bonuses box. These MUST be before talent modifications. So if you're getting 100 AP from equipping a new item and you have Master Marksman talent, do NOT put in 110 AP or it will count it twice! Crit and Hit MUST be percent based, not rating. RatingBuster should be in everyone's addons folder, if it's not that's your problem.
The pretty cells that normally show 0 next to important stats will light up a beautiful shade of green or red (depending on whether you lose or gain dmg) and show percentage difference your new stats will account for!
Please, please, please test these out, check formulas, post questions, offer suggestions etc. so I can make these spreadsheets more useful! It is still work in progress so don't make fun of me if I made a mistake
PS: When I averaged out FI and Frenzy I didn't take the spammability of Gore/Claw/Screech into account, so the overall BM damage is probably about 1% higher. Also I'm not sure exactly how very fast or very slow ranged weapons would behave in my spreadsheet, but anything between 2.6 and 3.0 speed should be fine.