I've not used this tool, but this guy on YouTube seems to explain the basics of it...https://youtu.be/W5hfAckBj3o
But, I do know a hell of a lot about how objects work in SMB. What specific questions do you have?
It looks from the video that you can neither create or destroy the objects of a level. That makes sense, because SMB has (almost) no free space in which to add new objects.
(If you truely can't delete objects...)
You could "hide" objects just past the castle at the end of the level, and use a "stop scrolling" command at the end to prevent the user from seeing those blocks.
Here's some random thoughts...
There is also a limit to how many things you can put on each page. Also, I can explain the "page flag". When the game is parsing a level, it will draw every object on the current page...until it sees a page flag, at which point it will start drawing objects on the next page.
There are 2 types of pipes. Active and inactive. You must set a new "area pointer" before the player reaches the active pipe, or else the pipe will just send you to the start of the level. If there is only one "area pointer" set, but multiple active pipes, they all have the same destination.
Multiple areas (underground/water/etc) can share the same level ending. You just need to put a pipe at the end of your area, with an "area pointer" that leads to that ending area (with a flagpole).
If you fall through the floor of a cloud world, its the same as going through a pipe...you go wherever the "area pointer" sets to go. If no area pointer is set, you go to the start of the level.
Using a level timer of "0" will put the remaining time from the previous level back up as the current time. If this was the very first level, it will = zero, and the game will be unplayable (instant death).
If you make a level from scratch, NOT using this utility, then it would be easy to add and delete objects...by hand editing the disassembly and reassembling. Ok. Maybe not "easy", but possible.
Also possible, but 1000x harder, the source code for the tool is available. I suppose you could add the ability to add/delete objects, by writing it into the source code and recompiling.