Since that is a stereo only unit with A/B speaker connections best you can do is connect up the main and surround speakers and leave the sub and center channel out.
You can try and connect the sub by getting a 2-channel mixer and using the line-out, that would effectively be similar to the LFE output on 5.1 but be full-range instead of LFE filtered and no volume adjustment (which is a major inconvenience!)
Possible to connect the DVD up to your TV and have the TV analog L/R output to the yamaha so you can listen to DVDs and CDs.
For your phone, there are a few ways to go: connect up your analog headphone out to one of the yamaha inputs (keeping volume low to avoid clipping/distortion), getting it connected to the TV using a streamer like chromecast or a lightning port adapter, or getting a bluetooth adapter to connect up to stream directly to the yamaha.
IMO much fustration can be avoided by upgrade to a 5.1+ AVR like the
Onkyo TX-SR373 for $200 so you can use all your speakers and have all the connectivity you need for your phone as well.