This is a guide on how to use the Precision Alignment tool mod that you can download here
If you have questions or I didn't go over something comment and I might be able to help you.
Usually you would want your precision alignment settings as shown here

Keep in mind that I don't know everything about how to use this tool but I know a fair bit. By experimenting and playing with the tool on your own, you can learn how to use even more than I share here. Or just be lazy and look it up on youtube :)

I strongly recommend having the Physgun Buildmode mod while using this tool. It can snap your prop to the nearest angle of your choosing (say 45 degree, 90, 12, anything you need) and you can change the angle snapping intervals individually for pitch, yaw, and roll. For example, I've used this to make sloped rooves at the exact angle. You can alter the settings for it in the q menu ->Utilities->User->Physgun Build Mode. I usually have snap position off and just use it for angles. Okay, back to the guide.

The very basics of this tool. Most of you will be fine with just knowing how to do this and not care about any of the other features this tool has. You will need to rotate the prop to the angles you want it at before moving it with this tool. While holding it with the physgun you can hold SHIFT and E together to snap the prop to the nearest 45 degree angle.
The selected prop will move in the direction from point 2 to point 1 by default. You can select a prop by right clicking it.

Points are color coded as red in the Manipulation Panel

• By default props will move from the last point you made to the first. You can select which points will be used and the order/direction in the q menu in the points table.
  
• Set point 1 at the position you want your prop at first by left clicking
  
• Set point 2 on the prop you want to move by holding shift and clicking. Hold shift until the point appears or else it will override your previous point
  
• Right click the prop you want to move. It should change colors
  
• Hold Q and click on "Move Entity". If you hold shift while you click this button, the prop will move and a copy will be left in its place.

You can get rid of the select color on the prop by right clicking the world. You can also clear the points by hold Q and clicking "Delete All" under the "Point" table.

You can also attach a point to a prop (This happens by default if you click a prop) to make the point move with the prop. Simply hold Q and select the point in the left table under "Point", select a prop, and click "Attach"

For most people, this is enough for them but this tool can do so much more.

I mainly use lines for offsets but you can also use them for other things like rotating a prop around an axis, finding the point where a line and a plane intersect, and more.

Lines are color coded as blue in the Manipulation Panel

You can make a line with start and endpoints at 2 positions with "Line - Start / End (Alt)" or make a line prependicular to the face you click with "Line - Hitpos + Hitnormal"
(With the first method you left click to place the start point and hold ALT and left click to place the end point)

Altering the line
Once you have your line press R and go to the "Lines" tab
Select your line by double clicking it in the top panel.
After changing anything click the "Update" button inside the panel that you changed and click "Set" to apply the changes to the line.
I mostly just have to change the length of the line. You can do this by changing the "Length" slider in the top right panel.

Getting the point where the line ends
If you are doing an offset such as placing a prop 100 units above another prop you will need to set the length of the line (See above).
Once you do that you will need to get the endpoint of the line (or startpoint but usually endpoint). Open the Manipulation Panel and go to the "Functions" tab. Click on "Line End Point", select the line and the point you want to set, and click "Set". Your point is now at the end of the line and you can move your prop like normal.


Rotating around an axis
Create a line and select a prop. Open the Manipulation Panel and go to "Rotation". In the bottom left panel select your line to use as an axis. Just set the angle and click "Rotate Entity" (Holding shift creates a copy)

Planes can be used to mirror build and do other things.

Planes are color coded as green in the Manipulation Panel

Creating a plane
Hold Q and select "Plane - Hitpos + Hitnormal" and click somewhere (Usually on a prop).
To change the direction of a plane use "Plane - Hitnormal" and click on a side of a prop if you placed it on one.

Mirror building
Place a plane in the middle of where you want to mirror (Usually in the middle of the center prop) and set the direction pointing towards the direction you want to uh... wait... here just look at the screenshot.
I want the selected prop to move to where the see through prop is so I aim the plane like so. The green line in the middle of the plane is where the plane is pointing.
Open the Manipulation Panel and go to "Rotation Functions", click "Mirror Across Plane", select the plane, and click "Rotate Entity" (Holding shift while clicking creates a copy).

Getting a corner point
You can get the corner of a map feature, the corner of a building, or anything else. For example, to get the inside corner of a house you are building, place a plane on the two walls of the corner and one on the floor. Press R, go to functions, click "Intersection of 3 planes", then select your 3 planes and a point and click set. This is useful for accurately putting something in the corner of a room, aligning something to the corner of a map feature, or other things.

Applying the last movement/rotation/mirror to a new prop
Hold shift while right clicking a prop and whatever you did last with the tool will happen to the new prop. Very useful for mirroring, rotating, etc.

Rotating
You can rotate a prop either by its center or by a point.

• Select your prop
  
• Select a point if you want to rotate the prop around a point
  
• Press R and go to the "Rotation" tab
  
• Select your pivot point if you are using one
  
• Set the angles to rotate by in the top left panel and click "Rotate Entity" (Holding shift will create a copy)

Creating constraints
Just follow the instructions given in the panel they are pretty self-explainatory.
You usually just need 2 points.

A little movement trick
You don't have to have the points on the prop you are moving. You can do something like this where you have both points on 1 prop (You don't have to have them like this) and the selected prop will still move the distance and direction of the points. So when I click "Move Entity" the big prop will move the distance of a 1x1 hunter plate.