Hi,
On Windows, certificates are generally stored in the Windows Certificate Store which is a combination of Registry entries and key files.
Our tool automatically stores the certificate in the windows certificate store then adds/updates the matching IIS website bindings based on the hostname mentioned in the binding and certificate. If you look at the Preview tab you will see the list of Bindings the app thinks match the certificate, based on their hostname or existing https certificate selection.
IIS https bindings should have the hostname set to match the website domain name, IP set to All Unassigned (not a specific IP) and SNI enabled. Any other combination is advanced and should be avoided unless you are an expert in https bindings.
Are you using your certificate with something other than IIS?