1) Speaker tweeters ought to be placed exactly on the vertices of a 3D equilateral triangle, the third vertex being the center of your head. That means, if center of tweeters are at about arm's length from each other (~70 cm, or 2.3') then each of them should be at that very same distance from your head/ears. Symmetry here is most important. So if not equilateral, an isosceles triangle would be next best, but preserve that symmetry.
2) Tweeters should aim directly towards your ears, and needless to say, with direct line-of-sight between those tweeters and your ears; no obstacles in front of them whatsoever. If needed, either tilt your speakers, or raise them a bit, or do both. Below a photo of my own little desktop speakers as example (ignore the dust and spots :P). Those bases under the little speakers are simple bean cans filled with sand + stones (each one weighs almost 0.7 kg,) covered with the cheapest self-adhesive carpet tiles from the hardware store. That short additional height makes the angled position of the drivers on these speakers laser-aim directly at my ears. Photo is taken from where my head would be. If raising the speakers, use something solid and heavy like that under them, nothing hollow, and nothing prone to wobbling or vibrating. I used those cans because couldn't find cylindrical stone bricks of the right height, although cubic ones were somewhat close.
The above two tips will already improve stereo imaging to better fool your ears into believing voices and sound overall (specially from good stereo recordings) magically come from a "sound wall" floating in empty space in front of you, and not from the speakers themselves.
If you also have a subwoofer, regardless of its size:
3) Try different positions for that little sub under your desk, to get better and more even bass response. In particular, try placing it neither so close to the back wall, nor to any side walls/flat solid surfaces, also not at the same distance from back and side walls.
4) Also raise the sub from the floor a bit using suitable bricks, and immobilize it for good against its own vibrations using more bricks on top. This will make the bass more precise and controlled within the normal capabilities of that sub. Changing its height will also alter the position of cancelling nodes for the low frequencies between floor and ceiling. Use isolation cushioning pads under the sub's feet, and under all those bricks. If yours is a carpeted floor, and you have a down-firing sub, get a large enough garden brick tile and place the sub or lower bricks on that. A down-firing sub should fire its sound against a hard surface, not a carpet.
Those last two tips aim to improve bass reproduction, increasing accuracy and removing the typical boomyness of desktop speaker sets that have a sub. Bass should be as clean and "normal" as possible from the sub in question, in any case not boomy or bloated, yet also not weak/muffled. Bass is always the trickiest thing because of room acoustics, but those changes alone can make major improvements.
To check bass response and sound reproduction in general, I suggest tracks like those listed in these posts:
Audio system testing tracks, Latin music edition
Audio system testing tracks, general
Bonus: 5) Improve the source. This is the only costly mod. To further improve sound reproduction, ignore all your PC's analog audio outs (PC's are electrically *very* noisy) and connect your speakers to an external USB DAC. I use an iFi Zen DAC, shown in the first photo placed below and behind the monitor. It's in fact a DAC and headphone amplifier. To listen with headphones, unplug your speaker set from the DAC/Amp and connect the headphones directly to that DAC/Amp (e.g. neither to the PC nor to a headphone out of the speaker set if there is any.)
To fully enjoy the music you love the most, try these tips. Doing so will get you the very best sound out of your desktop speakers, no matter their price range. Enjoy!
PS. Created a post on Mastodon about this topic. This text above is mostly a clone of it, just to document the same suggestions on this blog.