I use this boresighter:
Site-Lite SL-100 Mag Laser Boresighter with SRL-100 Rifle Scope Reticle Leveler - MidwayUSA
I also use this:
EXD ENGINEERING : EXD ENGINEERING VERTICAL RETICLE INSTRUMENT - World's Largest Supplier of Firearm Accessories, Gun Parts and Gunsmithing Tools
before hand so that I know my scope is over my bore, also using a bullet level on top of the turret to be sure the scope is level. Once I know that the scope is exactly over the bore and the scope (and therefore crosshairs) is level, I get to work. Some people also use a "hanging string" to see if their crosshairs are correct; either way works.
You can use a 25 yard mark, but I don't.
The garage door across the street is 100 yards away. I use this program: Handloads.Com Ballistic Calculator
to check how much my bullet is going to drop by 100 yards. As an example if I want the bullet to hit 2 inches high at 100 yards, and it's going to drop 2 inches by 100 yards, then I want the laser dot to show about 4 inches above the crosshairs when I project it on a 100 yard object.
Doing this I can get very, very close. Your horizontal alignment will probably be exactly correct but your vertical may vary a bit. This system has worked for me for several rifles in the past year. "YMMV"