The substrate isn't an issue with either filter. There is very little beneficial bacteria in the substrate unless you're running an under gravel filter. The vast majority of your bacteria colony is on the HOB filter cartridge and media. Are you going to continue to run the HOB filter along with the canister? If so, there really isn't anything you need to do. If not, put the filter media from the HOB into the canister and you will have moved most of the bacteria.
How do you plan to change the substrate? With the tank still running? Are you changing from sand to gravel, gravel to sand, gravel to gravel or sand to sand? Changing any substrate without draining the tank can put a huge amount of trash in the water and with sand can lead to cloudy water that takes a while to clear. If your current substrate is sand and you don't have live plants to keep it loose or haven't occasionally poked it to loosen it, you could have pockets of poisonous gas that you will release into the tank.
