Muxing is probably "the" most important function of MP4Box and therefore Yamb.

To access this, you must first click on Yamb's "Mux" tab:

The Audio & Video section

Your video and audio streams can be imported by clicking on the "Add" button [1]. If you have checked the "View Import Settings directly" box via the Options tab then an Import Settings window will appear (More detailed information can be found on this at this page). The  "Remove" button can be used to delete individual highlighted streams within the main list. In addition, the "Clear" button will completely delete all the streams in the box. If you wish to add some "Tags" for your output file, click on the appropriate button. More details about this can be found here.

The "Subtitles" section

It's not too complicated I must confess. Just click on "Add" button [2] to select your file. Yamb supports several subtitle formats, such as: srt (SubRip), ttxt (GPAC), sub (MicroDVD) or xml (mostly teXml QuickTime format). The drop down list allows you to confine your search more exactly.

The "Chapters" section

This is where you can add chapter break points to your file [3] . Yamb supports OGM chapters (as a text file) or GPAC chapters format.

At last, the "Output" section.

By default, the MP4 file extension is chosen. So in this mind, all you have to do is specify the path for your output file (otherwise Yamb will place your new file in the in the same folder as your first imported stream). If you would like to change the output folder, then a simple double-click within the "output" edit area will reveal an "Save As" dialog box. Which in-turn provides you with the possibility of selecting whether you want to save your file within the MP4 or 3GP container, via a drop down list. The name of your output file can also be edited.

Now.... if all everything seems to be okay for you, you can run the mux process by clicking on "Mux" button [4].

Hint: The max number of tracks allowed by MP4Box is 20. Any more than that and this tool wont work. One more thing: if your Audio and/or Video track is a 3GP file, Yamb will automatically change the output container format to 3GP