Hey bud. Even if the developed bb in your filter isn't enough to handle the load the worst case scenario would be that you have a mini cycle going on until the rest of the media you add is established so I wouldn't worry about it too much.
As far as removing substrate with tank running... Just did this today. Sand/Gravel combination. Practically the same as gravel. Here's what I did and recommend considering how ridiculously easy it is. Took an old 3-4ft 1" tube, 5 gallon bucket, and strainer to do. Put the strainer over the 5 gallon bucket and suck yourself a suction with the 1" tube and have it drain over the strainer over the bucket. It'll suck that gravel up in seconds. You'll be surprised how well... Anyhow, once the 5 gallon bucket is full or the strainer fills (whichever one happens first, usually bucket since 1" tube sucks fast) go dump the bucket water in tub and the gravel in the strainer into another container and keep going. I just plug the suction w/ my thumb so I don't have to keep getting a new suction every time. It works great when you have a second person to hold strainer and dump the water bucket while you hold the siphon. I bare bottomed a 45g 4ft long glass tank w/ 100lb of sand/gravel in like 10-15 minutes? I was selling the tank but guy was slacking his ETA and I didn't want to remove the fish until he got there but wanted to get all the substrate and everything packed, so yeah.
As far as adding the sand in, I didn't add any substrate in this tank since it was being broken down to sell but I have done this in my 125g. Same technique for removing, (was removing play sand), and once the PFS was rinsed I just slowly lowered the container of substrate into the bottom of the tank and then slowly release/dumped it onto the bottom. It was cloudy a bit and all the PFS settled over night np and was 100% clear in the morning.
