DiscJuggler supports many professional-level Audio CD features that are not immediately apparent to the end user, but are important for true audiophile-level reproduction. Among these features are the accurate duplication of gaps between tracks, index points within tracks, and the replication of the sub-codes used in digital audio. There are eight possible sub-code channels, referred to as P, Q, R, S, T, U, V, and W.

The most important sub-code channels for audio are the P and Q sub-codes. Sub-code channel P (or the "P" sub-channel) contains flags showing where music begins on a track. The "Q" sub-channel has information concerning the time of the start of the disc and current track. This information used by CD players for time displays is referred to as "position information". Track and index information is also contained in the Q sub-code channel. Finally, the "Q" sub-channel can contain an optional International Standard Recording Code (ISRC) for each track and an optional Universal Product Code (UPC) for the whole disc. The ISRC contains information about the country of origin of the track, year of recording, and serial number that uniquely identifies each track on a global scale. The UPC is a barcode functioning to uniquely identify each disc on a global scale.

The R-W sub-codes were originally intended in the Red Book CD-Audio specification to hold graphics information. Audio CDs with this kind of information are referred to as CD+G Compact Discs. Karaoke and Philips ITTS discs are examples of disc formats that use R-W sub-codes. Other information can potentially be stored in these sub-codes on audio tracks, but the Yellow Book specifies that these sub-code channels will be zero for data tracks. Sony introduced a standard to store Audio CD information using the R-W sub-codes. Referred to as CD-TEXT, this protocol uses the R-W sub-codes in the lead-in area of the first session to store information such as the artist, the album, the track titles, the genre, etc.