As telecubby said, gravel vacuuming doesn't significantly hurt or remove the bacteria in the gravel. Most of today's filters contain bio media within the filter which is probably providing most of the biological filtration anyway. Your Whisper does - it's the black spongy thing in the filter. (BTW, I think Dan meant it was a 115 Volt Whisper. We were looking for a model number - models numbers usually indicate the size tank the manufacturer intended it for, in gallons, or the flow rate, in gallons per hour. Whispers go by the former - for example, you may have a Whisper 10 intended for a 10 gallon tank.)
You should vacuum the gravel with every water change - if you have your vacuum out to siphon the water off, why not clean the gravel? If you've removed all of the water you wanted to, and you haven't vacuumed the entire gravel bed yet, just save the rest until next time - just vacuum different parts with each water change. If you're cycling, I suspect you're going to have plenty of ammonia in the tank to keep it cycling even if you vacuum the crud from the gravel, and vacuuming will help keep the ammonia and nitrites at safe levels until the tank is cycled. Start the good habits now.
I'm kind of surprised you've gone four weeks and see no nitrites yet. What kind of test kit are you using? Are you treating the water with anything? Cleaning the filter or anything?