The easy way to use Mils is to not think in inches or feet anymore. Put it behind you for now. Get used to thinking in the full mil and then the 10ths of mils. If this is not to your liking then go back to MOA or IPHY.
#1 always verify your zero before you do anything else! Otherwise when truing your dope all the info will be off the amount your zero was off.
I'm pretty simple minded so there's no way I have the mental energy to try to calculate inches to mils all the time to make sence of it all, and yet putting in good data into the ballistic calculator has enabled me to win many competitions throughout the years. Stick to "easy" and don't overthink things.
If you've got the scope height correct, which is center of bore to center of scope, the velocity, the BC, and the altitude correct, any of these ballistic apps will spit out a very close solution. If not then small adjustments to, BC, velocity, and scope height will line the dope up to exact or almost exact.
Next is understanding that if you have a FFP scope you can use the reticle to measure the POI from the POA to see if, or, how far off you are to make any corrections in mils. If using a SFP scope you'll need to do this at the one magnification the scope is true mils.