Folder structure for samples / buffers

I'm not seeing in the Bela IDE anywhere I can access folder structures, I've got many folders full of styles of samples, ordered by name etc.

It would be great to be able to keep these structures and not have to just plonk everything into the root of the project

Is this possible already? Or Should I use linux to access the beaglebone directly?

The IDE does not really support that. You can use a command like the following from your computer's terminal, though:

scp -r /path/to/folder/of/samples root@192.168.7.2:/root/samples

where you replace /path/to/folder/of/samples with the path to the folder of samples.
Would this work for you?