At this point, you should have your printer all wired and moving.
I'm going to try to explain this in text, but I really recommend watching the video for this.
You need to move the endstops so that when you "home" the printer, that is, tell it to move to 0,0,0 position, it's in the lower left corner of the print surface with the printhead barely touching the surface.
X and Y axes
The X and Y endstop switches are easy to adjust, and their position is not terribly critical. You want them to be pretty close to the lower left. You can get them in about the right place with power off, then power up and test them. Tighten them up when you're happy with the position.
Z axis endstop adjustment and print surface levelling
This is the fiddliest bit of building a printer. It's not complicated but it's a little maddening if it doesn't go well at first. You shouldn't have to do it much, but you will have to do it occasionally.
The Z axis endstop should still be stopping the printhead at least a centimeter over the print surface. We're going to fix that now. I'm assuming a hall effect endstop, which has a small adjustment on the electronics board.
If you're printing with tape, put tape on the surface now. We'll be homing to that.
I'm assuming that you are working with a fresh printhead and there's no old plastic on the tip. If you're coming back to this procedure sometime in the future when there is, you need to heat the hotend up then wipe the plastic off the tip with a paper towel, then let the printhead cool back down a bit - otherwise you'll be homing to a hunk of plastic instead of the print head.
Home the Z axis, turn off the power, then manually move the printhead back and forth across the X axis. If the printhead is higher or lower on one side, manually turn the right hand screw until it's close to level - we'll get it exact in a few steps.
Use a small screwdriver and put the electronic adjustment on the endstop in the middle of its control region.
Move the printhead back over to the left, turn the power back on and rehome the Z axis. Move the endstop down a bit at a time, then re-home the Z axis, until the printhead is almost touching the surface. Tighten up the endstop mounts at this location.
Get a piece of stiff paper, like a 3x5 card. Slip it between the print head and the surface. Adjust the electronic endstop adjustment up and down (clockwise raises the printhead detection point on standard hall sensors) and rehome, test and repeat until the paper card is just able to slip under with a little friction, but is not loose or too tight.
Now move the printhead manually to the right and check the position there. You'll have to hit "motors off" on pronterface to do this. Manually turn the right Z axis screw until you get the same resistance on that side.
When you move the right side, it affects the left. So now you need to go back to the left - be careful in case you adjusted it down a bunch and the head now crashes into the surface. Redo the homing procedure left and right until it's even from side to side.
Now you need to do the same thing front to back, except the adjustment here is to slip a little tape between the print surface and the plywood platform. I use blue tape, the full width of the platform, stuck to the plywood with the glass clipped on top of it. Again, just go back and forth, keep re-adjusting until you're getting the same resistance front and back. Now check left and right in the back. If this is not now the same, you may need to put more tape on one side or the other - normal window glass CAN flex a bit.
Keep playing with this until you're happy that you're getting a fairly consistent measure all over.
This does not have to be absolutely perfect, you can drive yourself nuts on this. The closer the better but you can make up for a slightly off print surface by printing a thicker first layer so don't sweat it too much.
Finally, you need to make sure that all the axes on your printer are orthogonal - that is, they're all at right angles to one another.
You can check the X and Y axes by homing the printer, then turn the power off. The print head should be in the lower left corner of the print surface. Use a Sharpie marker to make a little dot on the print surface just in front of the nozzle on the print head. Without touching the Y axis, move the head to the far right of the surface, make a dot there. Without touching the X axis, slide the print surface (Y axis) all the way forward. Make a dot there.
Now slide the print head out of the way and use a piece of paper or a square to see if those three dots form a right angle. If not, you'll have to jigger the Y axis. You do this by adjusting the nuts on the large 7/16 (M10) rod on the bottom. If the front of the Y axis needs to move right (if the angle was obtuse), turn the nuts on the right to pull the front right corner back a little. If it needs to move left (acute angle), do the same on the left.
If you have to move this very far (more than 1 or 2 mm), I'd recommend removing the wood screws holding the front Y axis clamp to the wood frame first.
Once you have the X and Y axes orthogonal, you can shoot in all 16 of the wood screws holding the Y axis to the wood frame.
You can now check the Z axis. This should be fine if you squared the frame at the beginning. To check, home the printer, turn off the power, slide the Y axis to the front, use a square up against the X axis rods and sitting on the print surface, and make a mark where the corner of the square touches the print bed.
Turn the printer back on and move the Z axis up to near the top (150mm to 200mm). Put the square back on. If the square doesn't hit the same mark, you'll have to shim either the top or the bottom of the Z axis smooth rod/motor holders. Be sure to shim the front and back the same amount. If you have to shim very much you may need to use longer screws.