For SMB3 pointers, you need to set 4 things:
1. Entrance horizontal - The horizontal range (x0-xF) of the pipe/door to enter.
2. Exit horizontal - The horizontal location of the pipe/door to exit.
3. Exit vertical - The vertical location of the pipe/door to exit.
4. Exit action - What Mario/Luigi should do once they arrive to the next area.
You determine #1 from the starting area where you're entering the pipe/door.
You determine #2, #3, and #4 from the destination area where the exiting pipe/door is located.
You set the destination area in the Level Header Editor, in the "Next area/Start" tab, in the "Pointer for next area of level" section on the left side.
To note, you can potentially have an area connect to itself. You can also connect to bonus areas like the worldly Underground areas that are generally for bonus items from the giant '?' blocks, or the worldly Plains areas that serve as endings with Goal Cards for some levels. You can refer to this post
for more information on the appropriate ROM offsets to change.
With your 3-byte pipe/door selected, look at the bottom-right corner in the editor to see 3 hex values. The second/middle value will determine the "Entrance horizontal" range. For example, in the original 1-1, the downward pipe leading to the bonus area has the following hex values: 27 8D 9B. 8D is its X offset in hex, and therefore, the pipe is within the 80-8F range.
Until you have figured out the *exact* spot that the exiting pipe/door will be in the next area, there's no real point in setting the pointer.
In the next area, select your destination pipe/door and, again, the second/middle value is what you want to get. If you're using a door system and there's no exit door (one-way) then you'll have to figure out the horizontal value of the exiting spot in hex. Either count, or click on a nearby object to check its horizontal value, and use it as a reference. Use the exact hex value you find for this setting.
In a similar fashion, refer to the following image to determine the *approximate* exiting spot for the pipe/door.
You will most likely have to place your exiting pipe/door around this value because, depending on the situation, there may be an undesired black/red-X sprite that will appear as Mario/Luigi exits a pipe, or Mario/Luigi might drop down if your ground isn't placed at the correct level. Therefore, some trial and error/testing may be necessary to get it right.
Depending on the objects that you're using to go from one area to the next, the "Exit action" will be different. They should be self-explanatory.
To note, "7 - ?" is for "Red Invisible Note Block" 3-byte objects (Bank 2, Type 7 (07)) that can be found in some SMB3 levels like the original 1-3.
Not sure if this covers everything for you, but hopefully it's something.