I don't know how many people have properly pushed the limits of the memory handler here, or indeed game specific handling for things (the New Super Mario Brothers folks did some stuff here).
For simple space finding then you have two main options
An older version of dsatm did something called deadbeef padding. Here the RAM is flooded with the value DEADBEEF (all hex) and thus you can then pop open the RAM viewer and anything that says that or a fragment thereof is presumably free at that point in time. Some games will clear it though, and with the DS being firmly in the sort of just about modern camp for game/program flow and doing some measure of dynamic allocation of memory there is always the risk of someone doing something strange (fiddling in options, stage select... compared to start at level 1) and the game overwriting something.
There was a fork of desmume that kept track of writes and would display it simply.
https://gbatemp.net/threads/unofficial-desmume-build-unused-memory-finder-tool.349332/
If I need to claw back some space in a binary I will tend to look for the wifi error strings. They are often in plain ASCII in it and a) wifi is dead and b) the replacement service probably won't experience the weird errors and frankly it does not matter if they do. How easy it will be to claw it back here for use with this I don't know, I would almost sooner fiddle with the handler to make it more of a dynamic setup if it is going to be that.
Afraid I have not played with Nitro Studio enough to know how well it works. I have not heard people pointing at it for use though, however plenty of things go unnoticed in ROM hacking world.
If you are having troubles with manual then you might instead try repointing it to the end of the SDAT (might have to change sizes of various sections too, though I would also not be surprised to find such values be redundant and included just because) and skip much of the repointing for later files issues.