My Honda activa scooter's manual say to add 800 ml of engine oil when the strainer screen is cleaned.I have drained all the oil and cleaned the strainer screen. I bought 800 ml pack of manufacture's recommended oil but when I poured new oil and checked the dipstick it showed the oil level at upper level even before I poured entire content from the oil bottle.I mean still there is around 100 ml of oil left in the bottle and the dipstick already shows upper level mark.Should I still continue to add the left over oil from the bottle or follow the dipstick ?
Run the engine, stop it, wait a few minutes and check again - there may be internal reservoirs that need filling : voids, pipes etc
As @SolarMike says in his comment - you probably didn't get all of the old oil out when you drained it, so there was probably some already in there before you started adding it from the bottle.
Keep the last 100ml for topping up later - as long as the level in the engine is between the marks you'll be fine.