So I went and moved into my secondary, I lost about .75 gallon of water to the yeast cake. Do I fill the secondary back up to the 5 gallon mark or no?
No.. Because what you lost isn't water, it's now beer. Never top up the secondary unless you just want to dilute what you've got. Next time, you brew more, and keep track of your losses. Thats why people struggle with all grain early. They don't know, or understand the losses from grain to the kettle, from the kettle to the primary, primary to keg/secondary/barrel/etc. If you add things it'll make more trub and you'll have to note that for the next time so you get as close to your final end product volume you wanted.
Not sure if you keg or bottle, but if you bottle, remember to take this loss into account when figuring out your volume for sugar additions.
Next time scale your receipe up a little bit so you end up with 5.25-5.5 gallons of wort after the boil. That way if you lose some during transfers you will get closer to 5 gallons of beer.
No, add more wort. Topping it off ANYWHERE in the process will dilute the beer. Extract brewers will do partial boils, have a high OG, and then add water to get back to their 5, 5.5 gallons and hit their OG. The recipe is formed with that in mind. You need to scale your recipe for losses, and make more upfront to lose it during the process. I regularly have to do a 7.5-8g boil, and by the time I'm putting it in the keg, I have right at, or around 5 gallons when I'm ready to drink it.
