Once a product is linked, a sale in either place counts on both. Switch stock sync on under Clover → Settings → Sync.
Sales in both places at once
Changes are added up against the count both sides last agreed on, never copied over each other. Sell one online and one at the counter in the same few minutes and you end up two down, not one. Saving a product on your website does not reset Clover's count either.
How quickly
Stores connected through the CloverWoo app hear about a change from Clover within seconds. Stores connected with their own Clover API token pull stock every 5 minutes, because Clover only sends instant updates to installed apps. Changes you make on the website go to Clover straight away in both cases.
Low stock
Set a threshold under Clover → Settings → Sync → Low Stock Alerts and you get an email when an item drops to it, whether the sale happened online or in the shop. Leave the address empty to use your WordPress admin email.
Counting by size? Track stock on each variation, or on the main product if Clover holds one item for the whole design. Whichever side has the item is the side that counts.