i just did 90 days report for my son (BKK) app was not working but Website worked well (did it late in evening and was approved very early next day) - so I recommend to use website instead of app
depends on your nationality e g Germany the old passport will only be made invalid at the moment you pick up the new one and they keep the new passport 6 month at embassy before they destroy it if not picked up - so better check with your embassy
Visa will not transferred only the stamps - so if visa is still valid (not sure if you mean your visa is multiple entry or you have a multiple re-entry permit stamp) you need both passports to travel