In almost every conceivable instance, playing back files in the native format you've purchased them from, is the best policy. DSD conversion isn't recommended as there is definitional contention concerning the state of "bit-perfect"-ness/lessless conversion to such a vastly different format. This isn't like a simple sample rate conversion that is very well handled these days by many converters. Though JRiver does fine with the DSD conversion, the question you should actually be asking yourself is, why you would want to even do such a thing in the first place. There is zero auditory benefit from things like upsampling or converting to DSD, you can't get anything out of it, but you can have a botched result with lots of out-of-band noise/distortion at worst.
If you have something like 24-bit FLAC files. You're basically using the best sourced file anyway. There's no reason you should be converting to DSD unless you just want to test out the claims of your DAC's capability.
If you're hellbent on getting native DSD playback (native as-in, not transfered over PCM, aka DoP), then what you want is DFF file format (though I would stay away from this conversion, as very few players can maintain the barebones metadata support it offers). DSF on the other hand is the true DSD format you want (metadata framework is far better and more interoperable to the few players that support it). There's another format called DXD (not really DSD, just simply a high sample rate PCM), but this is rarely seen and can be effectively ignored as it's somewhat used in the production side of things (if ever anymore honestly).
Also I'm not clear if you're talking about conversion and then playback (as I have been discussing up until now) or whether you're talking about the Ouput Format settings within JRiver's DSP Options menu to where you can choose DSD Native, or DoP (for temporary playback conversion). If you're talking about that, well then I'm not sure what JRiver is actually doing in terms of the encoders used for the Native DSD vs DoP option. The one thing about DoP is, you retain signal processing ability (meaning you can apply DSP and change volume levels, where for "true native DSD" output, you don't get to mess with anything from the signal, and will require hardware to even control volume output. So I guess "native DSD" is the thing you're looking for if you want "as true to format" as possible (whatever that means to you). But as mentioned before, since you're starting with a PCM FLAC file, this conversion can only degrade the signal at worst, and literally not change anything at best. Sound improvements? That's not going to happen in any instance.
The last part of your question.. I have no idea what you're referring to. "Setting to prevent any clicks or noise as I am listening to tunes that have some silence"? Are you talking about your DAC is making these clicks when listening to the same music regardless of source? (Meaning, are you hearing this when listening to the same song on Youtube, and hearing the same clicks and noise you hear as if you were listening to it anywhere else?). Some music can have that as part of the recorded material, or if it's a vinyl rip/version you could be hearing artifacts from vinyl scratch/pop and whatnot. But if you're hearing this from EVERY single piece of music that has silence, that seems to be a hardware problem from your DAC most likely or some driver-level issue from your computer, or it can be simply an electrical issue (if it's like a buzzing noise, then you have ground loops that people can get with busy electrical outlets in use by multiple devices, and that would require getting a balanced-audio setup which I won't go into here).
