The main point of using a "hidden" folder for your books is to avoid the processing into the kobo SQLite database. KOReader can handle books and formats that would corrupt Kobo's database.
When waking from sleep (with or without the cover) you return to the page you went to sleep on. Only when you actually poweroff, or exit KOReader do you return to the KSM menu. KOReader can be set to "Show hidden files" and "Start with last opened file". In this way you will be on the page you were last reading, when ever you start KOReader.
KSM can be set to "Auto select" KOReader, after a number of seconds you define.
Luck;
Ken
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