Dex,
I take the long road IE: C:\Program Files\Microsoft Games\Flight Simulator X\Addon Scenery\Misty Moorings\
folder for each different scenery in this case MM Nina's Landing I add the MM so all the RTMM sceneries are grouped together in the scenery library. Dumping all the .bgl into one scenery folder and .bmp, .agn, .dds files all into a texture folder makes it too hard to keep track for me. I prefer separate folders. Either way works fine just a matter of preference.
Now for Nina's Landing. I assume you read the posts about what I have done today vis a vis downloading the latest files and re-installing all of Nina's Landing. I had the same three .bgl files in my install plus a bunch more but have deleted them so can not give you the names but they were a bunch of Nina's_Sound_Gulls_Controller_FSX.bgl, Nina's_Sound_Gulls_FSX.bgl etc. two files for each different .fx file in the sounds. I followed the instructions but still wound up with these extra files in my installation some how. I'm sure the confusion stems from the way we are trying to do updates. It is causing extraneous files to be placed in the scenery folder. The most fool proof way to update is to provide all the files that are needed including files already in a previous version (if they are required) AND have the exact same file names for both the old and new files. First you simple delete all the files from the old scenery folder, to purge any that are defunct or updated, then copy/move the latest files into that folder. That way old files are replaced with the updated newer file and if there are new files never used before they are simply copied into the scenery folder. I understand that the scenery files and the sound files are separated entities but keeping track of two different sets of files only leads to confusion. We need to put both scenery and sound files into one download period. Now if there are some folks that simply do not want sound files the read me can tell them which files to then delete from the scenery folder of the appropriate scenery. This is why I use separate folder for each scenery. I saw very quickly that throwing them all into a 'master scenery folder' would be a can of worms for trouble shooting. When a given scenery and/or the sounds for it give a problem it makes it much easier to find and trouble shoot the problem. I think one problem with our readme file for scenery installations is that it is too all encompassing. It needs to be split into more than one read me. IE: Everything from the DESIGNER NOTES section to the INSTALLATION section in one read me and the INSTALLATION section and related text in another. Frankly most folks are not going to read all the info in the present one and just do their thing so to speak.
Now that my install matches yours I'll revisit Nina's and see what it is like.
PS: but not tonight I have been looking at Nina to the point I'm not gonna go there tonight.