LOKNLOD's explanation is very good.
You need to do some homework and have a better understanding of external ballistics before you dive right in. Inevitably you will get good and bad poop on the intarweb that can/will further confuse you.
Probably the most important take home point you need to remember is DO NOT TRY TO ZERO YOUR BUIS AND AIMPOINT TOGETHER. They are different sights, on different planes and work on different principals.
Zero your irons first. Level out your front sight post in the FSB. Center your Troy if its not already. Fire a group at 25 yds just to see where you're at. If you can't shoot groups at 25 then you need to put on the brakes and start practicing until you can. Any elevation adjustments will be made by rotating the front sight post in the FSB. Any windage adjustments will be made on the windage wheel on the Troy. I would use the small aperture on the Troy for zeroing. Others may disagree. If your end goal is a 50 yd zero your POI should be around 1-1.5" low from your POA at 25 yds. You can start making rough adjustments to get you close. Don't get wrapped up around the axle if its not perfect. If you can shoot consistent groups then move out to 50 yds and see where you're at. You very well may be spot on, you may not.
In my opinion (and this was taught to me) I would be more concerned about getting my windage as close to possible and accept a little more variance in my elevation. At further distances small variances in windage will only get bigger and be harder to correct.
BTW I would recommend zeroing your irons with your Aimpoint on the receiver however turned OFF.
Once you are satisfied turn on your Aimpoint and repeat the process. Ensure your Aimpoint is mounted correctly in your mount so that inputs will be consistent and repeatable. Zero your Aimpoint with the dot turned down as low as possible with the dot CENTERED IN THE MIDDLE OF THE SIGHT NOT SITTING ON TOP OF THE FRONT SIGHT POST. Again if you need to start at 25 thats fine. Then move out to 50 yds if thats your end-goal.
Once zeroed confirm at different ranges. At this point a ballistic program can be useful so you have an IDEA where things should be hitting at ranges however if you don't know the BC and velocity of the ammo you are shooting through your specific barrel then the dope becomes less ad less accurate.
Again, if you want to look through your sights and put the dot on the post and feel good about it fine but don't waste your time trying to shortcut to your zero. ZERO BUIS and your AIMPOINT INDEPENDENTLY. I'm sure others will disagree and thats cool too.
Good luck and get some real training. It will save you a lot of headache, time and hassle.

