We had no trouble securing the bikes at night. Usually the albergue/hotel/hostal would make certain we had a secure location to keep the bikes. This varied, sometimes the bikes were in our rooms, or the hotel kitchen, a spare room, a garage, etc. Take the usual precautions that you would take anywhere and things should work out.
As for stops during the day, we always locked them, or had one person stay with the bikes. In cases where we would leave the bikes to go tour a building, eat, etc., we carried all or our really important things (computer, phone, documents) in a day pack. I highly recommend the
Sea to Summit, Ultra-Sil pack. It weighs 2.4 oz/68 gm and it proved to be worth it's weight in gold. It stuffs into a storage bag that is about the size of a pack of cigarettes. It also served duty as our grocery/shopping bag and we never travel without it.
Enjoy your ride and report back on your experience.