You can always use a custom renaming pattern to create your own default season and episode number.
%ifseason%<RenamePatternIfTrue,RenamePatternIfFalse> - If season if greater than 0 rename using True pattern, else rename using False pattern (v2.4.2+)
%ifepisode%<RenamePatternIfTrue,RenamePatternIfFalse> - If episode if greater than 0 rename using True pattern, else rename using False pattern (v2.4.2+)
So it could be like:
S%ifseason%<%season%##,99>E%ifepisode%<%episode%##,99>
This will use the season number if it’s not 0 and set it to 99 if it isn’t available, similarly for episode so the result will look like:
If seaons and episode are available:
S1E1
or if they aren’t available
S99E99