The auto-numbering wizard available via Tools → Auto-numbering wizard... Ctrl+k allows for assigning tracknumbers and discnumbers to the selected files.

Tracknumbers

Begin at tracknumber

Sets the start index for numbering.

Save total count of tracks

If enabled, also saves the total tracks number. This field is prefilled with the selected files count.

Leading zeros for tracknumbers

If enabled, pads the tracknumber with leading zeros.

Please note that, e.g., MP4 tags store the tracknumber as integer value instead of a numeric string, so that leading zeros are not stored. Use the $num scripting function when renaming to pad with leading zeros.

Reset counter for each directory

If enabled, the wizard resets the counter for each directory it encounters.

Discnumbers

Begin at discnumber

Sets the start index for numbering.

Save total count of discs

If enabled, also saves the total discs number.

Leading zeros for discnumbers

If enabled, pads the discnumber with leading zeros. The same notes on tag format support apply as for tracknumbers.