Like you I have struggled with this but have found my own method which, whilst not technically pure, works without flaws. So here is my method (I have the Steam edition of AFS2 installed on my E drive).
1. Under the folder: E:\Steam\steamapps\common\Aerofly FS 2 Flight Simulator AddOns I have created the folder "Scenery" so it reads thus: E:\Steam\steamapps\common\Aerofly FS 2 Flight Simulator AddOns\Scenery
2. In the Scenery folder I have created country names (ie England)
3. In each country folder I have created 2 further folders (ie Images and Places)
4. In the Places folder I have created a folder called Cultivation
So far so good, and I hope you're still with me! Now to get scenery into the correct places I do this:
5. Download the scenery package you want (Izojub's scenery is a good place to start as it has everything).
6. Unzip (I use 7-Zip as I use Windows) as follows:
6a. Place all files from "Images" into the Images folder as in [ 3 ] above
6b. Place all files from "Places" into the Places folder in 3 above
** NOTE ** you will have to drill down into the ZIP file to get to the various map tiles and this will be obvious when you do: for example, the images may well be 3 layers down. However I just copy all files and if it asks to over-write, I just do. After all, cultivation is merely a representation, not the exact buildings, so I'm not too bothered with actual fidelity.
7. Make sure "Building Textures" from the Places folder has the following structure, for example:
E:\Steam\steamapps\common\Aerofly FS 2 Flight Simulator\AddOns\Scenery\England\Places\Cultivation.
That is, within Places there should be 1 folder that is called "Building Textures" - put the files from the "Building Textures" ZIP in here. The other files can just go into the Places folder - I just over-write when asked - as per my ** NOTE ** above.
As to airports from FSCloudPort they are normally provided in zipped download form ready-made in a folder structure (eg EGGP Liverpool). I just copy the whole folder straight into the Places folder as in [ 3 ] above and AFS2 finds them OK.
As I say, it may not be the "purists" method, but it works for me and I hope it helps you too. Feel free to come back to me for any clarifications.
Finally - enjoy!