3.1 or 2.1 Home Theater setup for desktop

If you really want a center channel, probably the easiest way to do this is get one of the higher end multi-channel sound cards, such as one of these:

Asus STRIX RAID DLX
Creative Sound Blaster Z
Creative Sound Blaster Live! 5.1
etc.

Then you'd have to find 3 channels of tube amp and 3 speakers, plus a power sub.  The 3 channel solution is a lot more complicated.  Of course, you can get a 5.1 channel computer speaker system.  Logitech offers several options.

The 2 channel route will get you better sound quality.  You can start with a high end 2-channel sound card such as Asus Xonar Essence STX II or EVGA NU.   Or you can look for an external USB DAC.  You'd have to get a power sub and then look for either powered monitor speakers or speakers+amp.

$1,000 is not going to get you very far here, unless you go on the cheap.

I should mention that it's meant to be on a desktop, but the speakers don't need to be desktop speakers, rather I expected to go the way of bookshelf speakers. I just want that sub for good low end sound, also I know a decent amount of setups tend to use the sub as a sort of crossover/filter (still not sure on the correct terminology) as it picks what freq's stay and which go out to the left and right channels.

If you really want a center channel, probably the easiest way to do this is get one of the higher end multi-channel sound cards, such as one of these:

I'd prefer to avoid any internal components on my computer as their very well might be issues with space/open slots as well as compatibility with Linux as I go between using linux and windows.

Look into Sonos Playbar and Sub, this combination is super easy to setup. I have yet to hear anything at this price range that can rival its superb sound.

I have been using this setup in two of my rooms for last 12 years and never felt the need to try anything else. Visit Sonos.com for many speakers options to pair with their sub.

https://www.bestbuy.com/site/sonos-playbar-wireless-soundbar-black/8028043.p?skuId=8028043

https://www.bestbuy.com/site/sonos-sub-wireless-subwoofer-black/5589100.p?skuId=5589100

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).