You should typically use Sections for creating the different Sections of your song. Then you should use Pattern Chain ( which probably should have been called Section Chain) and chain your sections together to make a complete song. Here are actually three ways to convert Pattern Chains to Songs on Motif.

1. You can store a Song Mix and then delete the Program Changes. (Recommended): Convert the Song starting at measure 1. Go to [Song] Mode and Select [Mixing]. Push the [Store] button, [Enter] and push [Yes] to Store the Mix. This stores the setting into a Mix and so the Program Changes are no longer necessary. Return to [Song] Mode and select [Job]. You can use the Event Erase function, Select Pitch Bend the Event to erase and All for the track. This will erase the Program Changes on all tracks in one macro operation.

2. You can move the Program Changes to a set up bar in Measure 1 of the Song.

If you want to export the song to another sequencer (where the MIX would not exist) or like working by keeping Program Changes in your Song, try converting the song again and putting it at Measure 2 of a blank song. Then go in to Event Edit (same method as above) and move the Program Changes to Measure 1 by selecting the event location and changing it. Remember when you do this if the event is blinking you have edited it and must push enter to make the change permanent. After doing this the sequenced notes will start playing fine at Measure 2 and you still have Program Changes in the Song.

3. You can create an Intro Section in Pattern mode with an empty first measure. The last way works if you have an Intro section to your pattern chain that is not repeated in the song again, you can just insert a blank measure with no notes at that beginning of that Section and then just convert the song at measure 1.

Take a look at the definitions of Sections. Patterns, etc. at: http://www.motifator.com/btm/btm_gettingstarted.html#2