You'd not need any upmixing if dealing with Atmos or DTS:X.
All formats will automatically utilise the associated codec to decode that format and no, you do not need to select the codec to be used. Dolby Digital will for instance use the Dolby Digital codec on the receiver to decode the audio irrespective of what upmixing mode is selected. Dolby Digital will still be subject to Dolby Surround or Neural:X upmixing because Dolby Digital isn't an object based 3D immersive format such as Atmos or DTS:X.
Note that if you apply Neural:X to DD+ ot TrueHD encoded soundtracks inclusive of Atmos metadata then the AV receiver will ignore the metadata and you'd just get the DD+ or TrueHD audio aspect of the incoming audio plus Neural:X upmixing. Dolby Surround would however be negated by the presence of Atmos metadata so you'd get Atmos sans any upmixng.
Each source retains its own mode/upmixing configuration independently. I'd suggest engaging upmixing relative to your TV source, but maybe engage STRAIGHT relative to a Blu-ray source.
Do I just crank it a bit more if I want to add the sixth & seventh channels, as it definitely does lower the overall impact, which must be affecting the discrete channels?
Master volume levels don't vary depending upon the upmixing or number of cnannels being portrayed.
THe calibrated levels associated with each and every channel are still in effect so your speakers are still calibrated and the volume scale represented is still the same relative to reference scale.
I'd suggest it isn't a matter of the levels and simply a matter of the processing Dolby are enacting upon the audio relative to Dolby Surround upmixing? TRy using the Neural:X upmixing as an alternative. Many suggest this has more impact than Dolby Surround upmixing.
I'd even suggest using one of the receiver DSP Programs as opposed to the SUR.DECODER upmixing modes if wanting to engage the presence speakers with non Atmos or DTS:X encoded sources. I find the DSP Programs to be far more immersive than either Dolby Surround or Neural:X upmixing. You'll also find that the dimished impact you are experiencing isn't the case when engaging one of the DSP Programs. I use the STANDARD program relative to all my TV viewing. I do however have one of the older Yamaha models that still comes equipped with Pro Logic Cinema upmixing, but do choose to use NEO:^ upmixing in association with my STANDARD DSP configurations:
I'd be more inclined to use STRAIGHT whilst viewing Blu-rays though and tend to switch between the STANDARD DSP mode and STRAIGHT depending ipon the audio if and when using Netflix.
I'd also be more inlined to use STRAIGHT or even PURE DIRECT whilst listening to stereo music sources.