E-Visa question

I applied for an e-visa last week however I was made aware that based on  my flight plans I may now need to enter Vietnam twice. My question is, I can apply on your site for a Visa on Arrival while also holding an  e-visa so that I have two visas to use for two entries? Or would I have  to wait until I use my e-visa on October 22 before applying for a Visa  on Arrival to use on October 25? Below is my schedule all arriving and  departing from SGN airport.I thought I would be able to transfer flights on October 22 without going through immigration but was told that this  may not be true. Any advice would be appreciated.

Oct 22: Arrive at SGN on Japan Airlines at 5:15AM

Oct 22: Leave SGN on Cambodia Air at 8AM

October 25: Arrive at SGN on Cambodia Air at 11:35

October 29 Leave SGN on Japan Airlines at 8AM

Many Thanks,

Michael