I'd try Yamb. It's a windows frontend for MP4box. If you don't have access to windows then I'm not sure what to tell you. In the admittedly little searching I have done I haven't found an ideal mp4box solution on mac. There probably is though.
If these 2 MP4's are from DVD (part 1 & part 2) and you have the DVD, you can use DVD2OneX2 to ultimately end up with a single MP4.
If these 2 MP4's are from DVD (part 1 & part 2) and you have the DVD, you can use DVD2OneX2 to ultimately end up with a single MP4.
However, if you all you have are 2 MP4s, you could use Quicktime Pro by pasting the 2nd one onto the end of the first one and then exporting a new (combined) file (though I'm not sure this will keep the chapter markers where they are).
Does anyone know how to bypass the compression used in DVD2OneX2?