Location of attachments
Is it possible to have Zotero store attachments in a directory of my choosing? I've set the base directory as a directory in my home folder, where I store my pdfs, rather than the default Zotero path. However, when I attach a pdf to a bibliographic entry in Zotero, it stores it in its own directory (e.g. Zotero/storage/66EULND2).
https://www.zotero.org/support/attaching_files
but this would cause loss of Zotero attachment syncing. You can recover some of this by syncing the new linked attachment folder by some other means, but not completely (e.g., no iOS syncing of attachment files, no group library attachment syncing whatsoever). It is much easier, functional and trouble-free to let Zotero handle your attachments.
https://www.zotero.org/support/preferences/advanced#linked_attachment_base_directory
People generally use a plugin to manage linked files - previously Zotfile (<= Zotero 6) and now zotmoov or attanger (Zotero 7). As noted, linked files have limitations - they don't work in the web library, Groups, or the mobile apps. But if you don't need those things, they work fine. If you need to access linked files across computers, you use a cloud-mirrored folder for those files (eg Dropbox, Google Groups). Zotero data syncing is turned ON (free/unlimited), and file syncing (usually) turned OFF (subject to online storage quota if used).
https://www.zotero.org/support/attaching_files#linked_files
As with all Zotero use, you should have good backups. And fully document your setup, in case you ever have to recreate it.