As far as flushing the block without removing the drain plugs, how's it done?
Details are in that link I posted above. Here it is again. Use the "perfectionest" procedures and you'll do an excellent job.
Cooling System Flush And Fill Methods For The Average Joe And The Perfectionest
Or what I should say is like where does the water go in at (where does hose go) and come out at?
You install the Prestone flush valve in a heater hose. The garden hose connects to that flush valve. You also remove the thermostat and open the radiator drain valve, as well as remove the "radiator cap", which is the pressure cap on the degas bottle. Then when you turn on the water, the tap water goes into a heater hose and flows through the engine and the heater core and back into the radiator, where it either drains out or overflows out the open degas bottle.
Do I do this with the water pump on or off?
On. Finish installing the water pump and connect the new radiator hoses before you flush with tap water from the garden hose.
I guess I'm thinking that flushing with water wouldn't there be a bunch of water left over inside because it can't get low enough to drain out.
There will be about a gallon of water left in the heater core after you're done. If you don't drain the block plugs, there will be another gallon or so in the block. But if you allow the radiator drain to finish draining, that will drain off almost all the water in the radiator. There will still be a cup or so of water in the lower radiator hose, but the procedures advise you to disconnect that hose and drain off that last cupfull or so.
After flushing with the garden hose until the drain water is clear, if you flush 4 times with distilled water, there will be almost pure distilled water left in the heater and block. That's what you want. Pour in the antifreeze concentrate then top off with more distilled water and you'll have the right concentration of distilled water and antifreeze.
Because of that gallon or so of water in the heater and block, you must use antifreeze concentrate instead of a 50/50 mixture. When you pour in 4 gallons of new antifreeze concentrate, then top off with distilled water, that will result in better than a 50/50 mixture.
Let's say I've just popped the hood of my truck, as far as flushing and changing coolant what's the next step (i.e. is flushing done before taking water pump off, etc.)?
Follow the procedures in the link above, modified because you are also replacing the water pump. First go to the stores (or internet for some items maybe?) and buy everything you'll need to getter done. In your case that includes the water pump.
Next, drain the cooling system. Then install the Prestone flush kit, remove the thermostat, and replace the water pump and the radiator hoses. Don't clamp the new radiator hoses until the end of the flush procedures. After the water pump is installed and buttoned up, then go back to the drain and flush procedurs and complete the job.