It has been up and running since the end of April. I just wanted to know if I could vacuum all of the gravel at one time (sometimes my bn plec doesn't allow for that messy has he is) or if I should just do half the tank (55 US) at a time.
Do you have lots of ornaments and/or plants? If yes then do all the gravel, if not then just stick to half one week and the other half the following week.
The beneficial bacteria, which are the ones you want to keep, are clinging to the surfaces of the gravel, filter media, glass, plants, decorations and any other item in the tank. It is not free floating in the water, and it is not in the gunk that gets siphoned out during vacuuming.
I wouldn't worry about getting rid of good bacteria; it will remain attached to these things. What you will be eliminating is the harmful bacteria that feeds on uneaten food and fish wastes.
And to be on the safe side, just your filter media in water you have just siphoned from the tank, but not unless it needs it.