Unlike extract or even partial mash brewing, doing well with all-grain mashing involves enough different variables that you really need a good reference text. What books, if any, are you using? If you don't have one already which covers all-grain brewing, I would strongly recommend picking up
How to Brew by John Palmer. It's an excellent book, more detailed and concise than Papazian's book while also more readable than Miller's (which was my go-to reference for years until I found Palmer's book).
The main difference you need to know about is
mashing. This is the process of coaxing the starches in the malt into solution, then letting the malt enzymes break them down into fermentable sugars. At it's simplest, It involves heating water to a fixed temperature (between 155 and 165 deg F) and adding the malt to it, so that you end up with a sort of porridge that is around 148-158 deg.F. This then needs to be held at that temperature for about an hour while the enzymes work on the starches. The exact temperature you'll need will depend on the type of beer you are making, and a difference of five degrees can make the difference between a dry beer and a full-bodied one.
The other major things you need to do, once the mash is complete, is slowly strain the water off of the grain, then adding more water to rinse the grain bed with until you have most of the sugars rinsed out of it. This process of straining (called
lautering) and rinsing (called
sparging) gets you to roughly the point where you would start at when beginning an extract based brew, though instead of having to add water, you need to boil part of the water off to concentrate the beer to get the gravity where you want it to be.
All of this takes about an extra two to three hours, and requires some additional equipment such as a larger boiler (at least 8 gallon capacity, for a 5 gallon batch), a vessel for holding the grain and water in while the starch conversion rest is going on (called a
mash tun), and a large strainer or separator (called a
lauter tun - many combine the two features into a Mash-Lauter Tun or MLT simply by having a spigot at the bottom of the mash tun that leads to either a false bottom or manifold). If you have the calculations right, you should have exactly a one hour boil ahead of you, though you could arrange for a longer boil if you choose to use more water. You would add your hops at the appropriate times, just as before.