Probably more of an opinion question as everybody probably does things differently.
I have a number of drives on my PC. A small but fast Nvme boot drive, a slightly slower Nvme drive for program files (other than music stuff, i.e. games library) a large SATA SSD for all my music stuff and two spinning rust drives for archival. All backed up to a NAS.
Now to the problem I like to install all my music stuff (DAWs, VSTs, sample Libraries, Kontakt, Decent Sampler) to the large SATA SSD, but I find that a lot of software (especially Kontak) is very very sensitive to file placement, i.e. a lot of the time it expects files to be on the C drive often hidden away in the /User directory structure.
How to you organise your software do you just let the software do a default installation?
It's getting quite frustrating adding in path information with still no guarantee it will pick up the latest instrument I've downloaded (especially Kontakt when not downloading from the official site, i.e. stuff from the pianobook community.
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I have the same issues, as my needs have evolved slower than a lot of the software, eg, Slate now comes with it's own programme manager for it's VST, and Spitfire does the same thing.
Often these come with a default path, which gets overwritten on an update ?, I'm not sure, but can see how it could lead to problems with certain patches.
As I said, it is helpful to actually have a folder structure written down, to see what might be missing, and there are plenty of videos around that show best practice for things like having Logic libraries on external drives.
Sometimes it is nice to have a new machine, as an excuse to set things up from a fresh state, using libraries already stored on externals, and then a faster drive will come along, and the process will repeat itself.
I then run a separate "Installers" directory with sub-directories for each package/VST/whatever that the downloaded installers go to.