I'm moving on to fly sparging and need some clarification
 

I'm using this calculator for the sake of example: http://www.brew365.com/mash_sparge_water_calculator.php

So I will heat up all of my strike water. Then I put the mash water volume amount in my mash tun with my grain. I then drain off and recirculate until it runs clear. I then drain the water from my HLT through my sparge arm over the grain bed and make sure I match the flow to my wort out into the boil kettle?

Do I let the initial mash water sit with the grain for a set period of time before beginning this process? When do I start timing the mash? Do I need to stir the mash for awhile before I start the sparge?

Thanks for the help, I couldn't find a definitive answer.

You're going to heat your strike water and dough in like normal. let that recirculate if you want for the length of your mash. Once you hit your mash length, you set the flow of the sparge to be the same speed as you are collecting in your kettle. That's about it.

Ok, so basically I let the initial mash water actually do the conversion then the water from the sparge is to help wash away the converted sugar into the wort?

exactly. well, wash off any sugars that are clinging to the grain.

Yes, assuming you're using a single step mash. It's no different than a batch sparge, except with a batch sparge you "rinse" the grains by refilling the MLT and draining again, whereas with a fly sparge you hold the grains essentially in suspension and flow clean water through them to pick up any sugars left behind by the mash. Either way, the starch conversion takes place in the same way.