JRiver does not do anything with HDCD disks. It just reads them at 16 bits. dBpoweramp will decode them to 20 bits. Then JRiver will play the 20 bit data. I have not done it is a while, but there is an option to turn on HDCD decoding somewhere in dBpoweramp. It uses the hdcd.exe reversed engineered program, I believe.
You may have figured this out, but here is some info for you.
In MC a library is a small folder that contains your custom data (like view layouts, output devices, etc.) and a pointer to each media file. The library should be on a local, internal disk. The media files can be anywhere as long as the access is fast enough. So, your media files can go on your NAS. When you import the files, you just use its network name or a mapped name.
I believe you have at least 2 PCs. You need a copy of MC on each PC. You have the choice of maintaining a full library on each PC or just having the main server library have everything, in which case the client PC has a very minimal library. Maintaining full libraries on each PC is extra work, in that any changes to one PC has to be duplicated on the other PCs. If the PC clients are going to just be just playing or viewing the music/video, then client/server is probably the way to go. You just then just use your main system as the one to make changes and to import new media files.
To set up a client/server, start by setting up the MC server system to share data. Go to Tools/Options/Media Network and turn on Media Network sharing. It will show a code of upper and lower case letters. You use this on the client to connect to server. You also need to provide the server login and password information. If you know how to do it, setting up a static IP for the server is a good idea. If the router changes the IP address of the server, the clients will not be able to connect to the server.
On the client, select Playing Now and Add a Library. You select a name for the server and enter the code. That should allow the client to download the library from the server to the client, temporarily. In playing now, you select Player (the default) to listen/view on the client. You can also use this mode so the PC acts like a remote control and plays the media on the server. You do that by choosing There from Playing Now.
Changes made on the server generally propagate to the server, but if yo make changes on the server, it may be necessary to have the client load its main library (mostly empty) and then reload the server library to get the new information.
JRemote can also connect to the main server using the same code and play/view on an iPad/iPhone.
I would set up a sever with some files and try client/server mode (known a Tremote - since is was originally viewed as a Terminal Remote to control the server system). There are lots of nuances, but that should give you an idea.
Using S/PDIF from the Lenovo to the EE DAC should be fine. Use WASAPI, Kernal Streaming or ASIO for best sound. You select the output device in Tools/Options/Audio Devices. JRiver to your EE DAC to your McIntosh system should sound great.
Sorry if you know all this, but thought it might help.