This guide was made for Valve Hammer Editor 3.5 but it'll apply to any of its derivatives such as JACK.
I write this hoping it'll help any new mappers to familiarize themselves with the standard tools of the editor.
Just your standard selection tool. With it active, you can either click on stuff in any view to select them, or you can make a box selection in any of the 2D views to select multiple objects at the same time. Just click-and-drag to start creating the box, adjust it in the other views, and finally hit Enter to apply the selection box! SELECTION TOOL (Shift+S)
With one or more objects selected you may click-and-drag to move them around, or drag the handles to resize the object(s).
Click the selection to cycle through various modes. The next one has circular corner handles that will allow you to rotate the object(s) (hold Shift to rotate in increments of 15°). After that is skew mode where box handles at the center of the edges will allow you to skew the object(s).
With the tool active, left-click in a 2D view to zoom in, right-click in a 2D view to zoom out. It doubles/halves the magnification for every click.
Activate the tool and click-and-drag in the 3D view to look around. You can also place and aim a camera in the 2D views by holding Shift and click-and-drag the left mouse button, the initial click sets the camera position and where you let go of the cursor is where its endpoint will end up. This endpoint is where the camera will be aimed towards. You can adjust either of these points in the 2D views, and the result will be shown in the 3D view. CAMERA TOOL (Shift+C)
This tool lets you place entities in your map. You can either click anywhere in the 3D view to place an entity right on the surface you clicked on, or you can place entities more precisly by using the 2D views. Click anywhere in any 2D view to start placing the entity and drag the box around to adjust its position. Optionally pick the type of entity you want it to be from the Objects list. Press Enter to finalize it. ENTITY TOOL (Shift+E)
This is your main tool for crafting your world. Click-and-drag in any of the 2D views to initialize a box. This box will be the size and position (i.e. bounds) of the object you wish to create. The Primitives Category will have some basic shapes that you may use to create your brushes, the building blocks of the map. The block shape will be the primary Object for creating your map, the rest will mostly be used for decorating. Press enter to finalize the brush.
BLOCK TOOL (Shift+B)
Clicking this tool opens a pop-up where you can adjust the texture and its Scale, Shift and Rotation etc of any face that you select in the 3D view. Right-clicking with this tool open will apply the Current texture to whatever face you clicked on. TOGGLE TEXTURE APPLICATION (Shift+A)
At the bottom of the window you may select one of many different modes. Instead of describing what each mode does I'll just explain what the terms mean:
This uh, just applies the Current texture on the selected objects. That's what it does. Not sure if there's anything else to be said about it.
APPLY CURRENT TEXTURE
The proper way to apply decals. This will automatically place an infodecal for you using the Current texture on whatever brush surface you clicked on in the 3D view with this tool active. APPLY DECALS (Shift+D)
One of the main tools for modifying the shape of brush objects. It works by defining a Clipping Plane (a flat sheet in 3D space) which will be the knife for cutting up your object. First select the object you wish to cut up and then activate the tool. Now click-and-drag in the 2D view you wish do perform the cut in. Manipulate the handles until you're happy. CLIPPING TOOL (Shift+X)
Before we're done, the Clipping Tool has 3 modes that can be cycled through by clicking the tool icon (or pressing the shortcut Shift+X): keep first half, keep other half, or keep both. In the preview you can see what will be kept has a white outline and what will be discarded will have a red outline. Press Enter to finalize.
This is your other main tool for modifying the shape of brush objects. As the name suggests, it allows you to manipulate the vertices of the object. It also makes it very easy to create invalid shapes as the tool doesn't stop you from, say, placing vertices off-plane. Select the object you wish to manipulate and activate the tool. In the default mode you can click-and-drag to reposition vertices or edges in the 2D views. If multiple vertices/edges are selected due to sharing the same 2D position, you can use the 3D view to get a more specific selection. VERTEX TOOL (Shift+V)
Clicking the tool icon (or pressing the shortcut Shift+V) will cycle through its modes where the next mode will display the vertices only. The third mode will only display the edges. Exit the tool by by activating any other tool to finalize.
This tool provides an interactive alternative to placing path_corners or path_tracks to create, well, paths for trains for NPCs to follow. Start by activating the tool, then hold Shift while you click-and-drag in a 2D view to define the starting point and next node. It will activate a pop-up asking you to provide a name for the path (which will also be the name of the first entity) and whether its Direction will be One way, Circular (last node will point to the first one as its next node), or Ping-pong (reverse and travel back to the beginning after reaching the final node). Hold CTRL and click-and-drag from the last node to create a new node. Each new node will be named <path_name>01, ...02, etc. PATH TOOL (Shift+P)
It has been reported to be buggy and inconsistent and most mappers prefer placing the path entities by hand. I tried this tool for myself while writing this and, while it did create a working path_corner path for a func_train to follow, the final node did not point back to the first node as would be expected of using Circular Direction. It also did not give me the option to manually set its Next stop target.
I hoped this guide has been of any help!