Hi,
For Aquasuite software settings just export your pages to disk and then import them after the install. If you have any custom graphics etc remember to keep them also. These by default go into your C:\ProgramData\aquasuite-data folder
For each hardware device such as pump or Aquaero go to it's system settings and "export active settings to file" then import after the install. These by default go into your Documents\aquasuite\profiles folder
I've done it multiple times with no issues.