Newly added or enabled autocompletions should be visible within a few hours.
If a few hours have passed and you still don't see any autocompletions, make sure you have included an appropriate set of sites in the Sites page for your CSE. Autocompletions will not currently be generated based on sites included indirectly via annotation feeds. Google generates autocompletions based on popular queries for search engines. If you've set your search engine to search the entire web, autocompletions other than custom autocompletions you add yourself may not be available to display.