I noticed my batch in the secondary looks short of 5 gallons, can I top it off with water when I bottle?
I wouldn't bother, unless you have a specific reason. If you think the beer is too strong and needs to be watered down, go for it. If you are worried because you are a half gallon off, but the beer tastes fine, don't worry about it! I've often been off by a quart or two, and the beer still came out great.
If you do decide to add water, be very careful. Make sure the water is free of microorganisms (bottled water is your best bet) and be careful not to introduce oxygen to the beer (siphon the water in, don't pour it).
My first batch was supposed to be 5gal. I primed it as such and realized that I only had 4gal collected in my bottling bucket. I lost the other gallon to poor technique I guess. Anyway, since 4gal carbed as if it was 5gal is significantly different than a normal 5gal carbination, I added a gallon of bottled water at bottling. The beer turned out fine, sort of like a low-alcohol Pale Ale. It was thinner than I wanted, I suppose, but was still tasty.