3.1 or 2.1 Home Theater setup for desktop

The problem with Sonos is that it only has HDMI/optical inputs.  No USB input.  Plus, if you really want a sub, $599 will get you a rocking Rythmic sub which is going to be a lot better than the Sonos for the same price.

I would do this in stages. Look for a USB DAC with a volume control.  These are a couple that are not too expensive (for what they are), but are about half your budget.  You can get them for less used on ebay or other sites:

Parasound ZDac
Cambridge Audio Dacmagic Plus

Both of these or USB DACS and have both XLR and RCA outputs that can be used at the same time.  Look for some nice powered monitor speakers.  Think Yamaha HS5 or other powered monitors.  You can add a powered subwoofer of your choice at any time in the future using the second set of outputs from the DAC.

Alternative, you could go for that tube amp and look for some nice bookshelves (Elac is the only one that comes to mind that is cheap enough but still very good).

auxinput,

You do not need USB input with Sonos. If I read OP requirements correctly, he will be connecting Sonos Playbar with his TV and for that all he need is optical input.

I am sorry to say, everything you have suggested has ‘clutter’ written all over it. Consider wires, space and synergy between the desktop speakers, sub and DAC. And then look at two piece Sonos setup.

For a compact 3.1 system with a sub, there isn’t anything better than Sonos. Great app, wireless connectivity Unless you try and listen, you just never know it’s true potential.

you will love a darn good office system.

I just set up my office, best sound I ever had here. first, I rebuilt/re-positioned my desk to allow a perfect equilateral triangle with my mains which are non-ported bookshelf speakers. I picked and bought used B&W D100i. (6-1/2" woofer size).

My desk is pulled back away from bookshelves on front wall, creating the triangle, leaving an aisle to access the shelves, but importantly allows locating my self-powered sub, old velodyne 12" re-coned, on the floor between the shelves and desk, tucked back, aimed sideways, simply adding low bass, not directional. I just add a bit of bottom with the sub, unaware unless you turn it off. wires from computer to sub, to adjacent bookshelves.

get the tweeters seated ear height as always.

separating low bass to the sub first, sending the rest to the amp/bookshelf mains is good, the amp and mains do not need to try and produce low bass.

four advantages:
1. bookshelf mains do not try to make low bass.
2. not trying to make low bass is how you successfully avoid bookshelf speaker designs relying on ports to try and make low bass
3. amp can be lower power, smaller, more affordable, more location options.
4. sub’s amp can be powerful to control woofer without costing a great deal.

I love tubes for my main music system, but you may want to rethink tubes, because the computer is on a great deal of the time, even when out of the office (the kitchen!), and when working, not listening, making heat, burning watts all the time.

I would not add a center channel to the mix, just get yourself the best centered listening position.

Prior to this, I was off-center and relied on the balance control to center things, ok, but centered for real is wonderful.

Video images perfectly centered to the sound is terrific.

To add to this. Seeing as 1000 isn't necessarily enough to build a whole system. Any recommendations on a start to building a whole high-end system. Maybe like a DAC, amp, and two bookshelf speakers with a path to get a sub later or DAC w/ amp and speakers with a path to later get a better amp and sub? This is all new to me, got a lot to learn so any help is appreciated.

@lalitk - "thatcdac" stated that these would be used on a desk and titled his post "desktop".  In a later post he somewhat confirmed his position on computer because he does not want to use an internal sound card on his computer because of technical reasons.  This leaves only the option of a USB DAC with a volume control.  I do not see anywhere that says this is a normal TV/entertainment setup.

@thatcdac - I agree that tube amp is not really recommended here.  You could go that direction, but the budget is going to be more like $1500, and that does not include a subwoofer.  Also, tube amps are going to be low power and tubes will start to saturate once they get past half of their power rating.

I'll repeat my initial DAC suggestions here (they are in the $500-600 retail area, but can be found for less used):

Parasound ZDac
Cambridge Audio Dacmagic Plus

The Parasound ZDac has a better stock power supply (internal linear power supply), but ZDac can only support audio files up to 24/96 resolution on the USB input (24/192 is not supported).

Cambridge Dacmagic Plus will support the higher 24/192, but comes with an external switching power supply adapter.  So the stock sound quality will not be as good as ZDac, but you can always upgrade this to something like a Teradak linear power supply (another $200-300).

For speakers, the easiest solution is to get powered monitors (speakers that have the amplifier built in).  My own personal recommendation is the Yamaha HS5, which retail for $400 a pair.  You can look at others if you want.  Then just get a couple of XLR cables and connect the DAC directly to these speaker - and you're done. 

Cost for this solution is about $1,000 (or just under).

Alternative, you could do a set of normal speakers and an amplifier here, but the budget is likely to go over $1,000 (probably something like $1200-1400).  Low cost amps are stuff like Parasound Zamp ($350) or Emotiva BasX-300 ($399).  Plus speakers.  A low cost bookshelf speaker that still sounds very good would be something like Elac Debut 2.0 B6.2 at $349).

These are just different ideas on approach.  With these two DACs, you can always add a subwoofer to the system later on at any time.  A really nice reference subwoofer for the money is Rythmik Audio L12 for $559.  It's not really huge compared to other subs (14" x14" x 15.5"), but Rythmik is one for sound quality.  There are smaller subs you can get and also cheaper subs.