Just read this and going to give my +1 to a few suggestions:
1. You need to assign inputs to your various sources, e.g. if you connect your CD player via a coaxial, RCA or fiber optic, you need to set the receiver up so that when you select "CD" on the receiver, the receiver knows which input its supposed to process. This goes for all the sources, which are set by default to the HDMI inputs as labeled on the back panel.
2. Try to use the DAC inside the receiver for all decoding. That means setting up your sources to output undecoded "bitstream". Note that the term may changed from device to device. I did this with my BDP and HTPC and it ensured I got Atmos properly and stopped audio "snap crackle and pop" on some BD playbacks. My only caveat would be that if you prefer using your CDP's DAC you have to use the analogue inputs (RCA cables) and assign the input as in 1 above.
3. The Marantz units display "Dolby Digital" when playing Atmos sources. There's a button or two you press on the remote and it will show you what the source code is providing and which speakers the receiver is driving in response though.
4. 125 watts vs 150? You'll barely hear a difference. What using an external "proper stereo" amp for your fronts will do, however, is (a) possibly give you better sound for "proper stereo" sources like CDs - if they are connected directly to the "proper stereo" amp and not via the receiver; (b) enable the receiver to deote more if its power to the other channels.