Export Audio: Entire Mix vs Main Outs

"Main outs" and "entire mix" and the other source choices just pick the set of (in use) buses that are listed in the source buses/tracks list box. The entire mix choice prevents deselecting any of the listed buses (i.e. its a preset for everything going to the hardware mains) but the main outs choice allows you to pick and choose which mains you want. Then the bounce process will add an internal mixer(bus) which sums all the listed bus sources. 
 
So "Main outs" and "entire mix" will be identical as long as you do not deselect a source in one case.
While entire mix not always what you want however. SONAR has no way of knowing the difference between a headphone mix or a submix sent to another set of speakers so entire mix will sum all the buses listed which is probably not what you want in that case since you are duplicating the mix.
 
Generally its a good thing to look at the sources being selected and make sure that it only includes what you want in the final mix. As Kalle says, the most deterministic choice is to make sure that all your tracks and buses ultimately route to a single bus (such as the default one called Master) and then when you export, choose that bus as the source. An easy way to check this is by looking at how many buses are listed when you pick the "Buses" source category. If you see more than one then you have multiple destination buses - typically a headphone mix bus will do that.
 
Also something else to keep in mind. The main outs typically go direct to the speakers via the audio interface. One use of the main outs is to change the gain at the main outs to make the listening level louder or softer. If you have ever done this then the mix from the main outs will be different from the mix coming out of your "Master" bus. Also if you had tracks directly outputting to mains (intentionally or by accident) this will definitely make the two mixes different.