Congratulations on getting a DAVE. I agree, reading through nearly 6,500 posts is not an easy undertaking. The most important posts are from Rob himself. Start there.
In almost any setup you come up with, DAVE will not be the limiting factor or the weak link and so while DAVE will improve almost any system it is placed in, with proper care and attention, you will find it will have much more to offer. It depends how high you want to take it. While talk about Davina, Blu mk2 and Chord's new digital amp can be distracting, these units will be designed to especially shine on the DAVE and will allow the DAVE to show its truer potential and as these devices are expected to be released in the coming months, their discussion on this thread will probably be inevitable.
For speaker use, the single-ended outputs are a bit more transparent but balanced outputs sound excellent so go with what your speaker amp prefers. For headphone use, feel free to experiment with other headphone amps and go with what sounds best but I believe you will find that nothing will sound as transparent as connecting your headphone directly to DAVE's headphone jack.
There aren't a whole lot of settings to concern yourself over. With the HF filter on, you get a touch more smoothness but at the compromise of timing. Go with what you prefer.
Same thing with crossfeed. This is obviously applicable only to headphone listening. There's no right or wrong and you will find people will have different preferences or no preference at all.
Regarding the phase switch, you'll be surprised to find how many recordings are out of phase which can lead to a thinner and more bass-shy sound. Out of phase recordings can also sound more diffuse with poor localization of instruments. If you question the quality of what you're hearing, try inverting the phase.
PCM Plus and DSD Plus are self-explanatory. Unfortunately, you have to toggle from one to the other when you go from PCM to DSD if you want either to sound their best and there is a normal gap of silence that ensues as the DAVE switches from one mode to the other. While DAVE plays back DSD very well in my own experience, it is well documented that Rob much prefers PCM and that he believes with everything else being equal, PCM at 16/44 sounds better than even DSD512. I happen to agree with this and so the only time I seek out DSD recordings are if they were natively recorded with a DSD recorder.
While it has become very chic to upsample PCM to DSD with HQPlayer, feel free to try it yourself and see what you get. I believe you will find that DAVE does a much better job upsampling than HQPlayer. Feel content to send DAVE a bit-perfect signal and let DAVE do the rest. The exception to this would be digital equalization to correct for deficiencies with your headphones or speakers. JaZZ can tell you all about what a difference this can make.
Should you decide to connect the DAVE to a preamp or an amp with its own volume control, you would do best to use the DAVE's volume control. It is completely lossless and you won't find anything that will attenuate better.
As far as digital inputs, they all can sound good but Rob will tell you that USB sounds best followed by Toslink and that BNC has the potential to sound the worst. With BNC and AES/EBU, the quality of the cables matter more as these inputs aren't galvanically isolated.