HI David,
1. To your first question, deleting photos in any of the Lightroom (Lr) apps will move them to the Deleted files section of Lr, where they can be recovered (if accidentally deleted) for 60 days.
If those are full resolution photos AND you were syncing your Lightroom Classic (LrC) catalog AND syncing had completed, then the full resolution copies would have downloaded to the computer running LrC. Deleting the photos in Lr will not delete the full resolution copies downloaded to LrC, but those deleted photos will be removed from being synced with LrC.
I find it easiest to manage cloud storage using the desktop Lr app for Mac/Win. Here's a tutorial that shows why it is easier there: https://lightroomkillertips.com/using-lightroom-cc-desktop-window-cloud-storage/
If those 1,000 photos (or some number of them synced from LrC originally, then they are just smart preview versions of the originals in LrC. Deleting in Lr just removes them from being synced. Smart previews synced from LrC do not count against your cloud storage.
2. You can only sync photos from LrC to Lr by putting photos in a collection that is synced or by drag/dropping photos onto All Synced Photographs in the Catalog panel. So, just make sure you did not inadvertently mark collections to be synced that you don't want to be synced.
On your iPhone, open Lr, go to App Settings > Import and verify that all options under Auto Add from Device Photos are disabled, then it should not be auto importing photos from your Camera Roll.
3. If you want to sync a small batch of photos from LrC to Lr (which again, are just smart previews and excellent for editing and sharing to social media), then with syncing enabled from LrC, add photos to a collection that is already synced or create a new collection and mark it for syncing to Lr.
If you import photos directly into Lr on your iPhone the full resolution photos will be uploaded to the Lr cloud and count against your storage and will (eventually) download full resolution to your computer running LrC.
Here's a tutorial you may find helpful: https://lightroomkillertips.com/getting-started-with-syncing-lightroom-classic-to-the-lightroom-cloud/