Vacs do an excellent job of removing silt, sediment and leaves from the bottom of the pond. Hoover like you are using a vacuum in the house, move the section nozzle along the bottom of the pond in a gentle motion to try and prevent string up dirty and loading your vision. There is no need to remove the fish from the pond. The vacuum will remove water from the pond at the same time as the dirty, so make sure you have a suitable location for the dirty water to go. Some models will turn off to empty and then back on to resume suction, others will remain on constantly as they have 2 chambers.
All models sold will discharge the dirty water to waste - the water cannot be put back into the pond. Once you have finished the cleaning the pond will need refilling, ensure you use a dechlorinator when topping the pond back up.