4 Ways I see of doing this
1. If possible change your volume in the card slightly down, if it's set to 24bit and you are playing 16 bit audio windows volume will not lose quality unless it's taken down a whole lot, lower it til you get a bit more useable room (don't just drop it as low as possible though and crank up the magni, a Magni past 3 o'clock is just insane, your source may be low but noise will be amplified.
WARNING: Don't do this if you use 24 bit music as it'll cut the bits into bits. Well it won't sound in theory, in practice, up to you I guess
2. A lot of IEM users used these little -16db attentuator (I'm spelling it wrong but google will save you) these just set the volume lower from the source by putting resistors in the way, I have not done this but it seems like a nice option. They are little RCA Plugs that just plug onto an end of the cable and make the cable harder to drive basically, it'd be like splitting the signal and attaching headphones that would eat up your soundcards output voltage from the RCA ports. (not sure how much more volume control that equates too on the Magni)
3. Use the SYS as a volume control (and add possibilities for other sources to be added to your Magni too.) Works somewhat like the above way but I'm really not sure how great of a solution it really is.
4. Ditch the original Magni (or keep it as an extra bedside or amp at work or something) and get something like the Magni 2, which has a gain switch, so you get the same sound as the original Magni, but now with a nice gain switch (sadly I asked around, and talked to Schiit and they said there is no way to change the original Magni's gain, the new one has a different circuit board.
NOTICE: It appears the Magni 2 has a different chassis color than the original Magni so let's say if you had an original Schiit Modi or just preferred it matching any other older Schiit gear this is what I'd do:
Keep original magni, buy Magni 2, put Magni 2's cover on Magni 1, and put Magni 1's cover on Magni 2.
LEGAL disclaimer I am not liable for any loss of warranty or death if you do something wrong in the case of what I would do on the 4th option, which is my favorite.
Also could look at the Objective2 Amp, not as pretty not made by Schiity, battery operated as well, and no longer One-Fitty. It's currently 130 (without power cable) I have to Magni cables so I might get the O2 or the Magni2 if I get a bit more spare cash to waste.
The O2 does look appealing, but a few turn offs, 3.5mm jacks unless you pay more to change it (JDS Labs let you change things for added cost) Power in the back (+$3), stock power is front, 1/4th inch headphone output (+$30) Rear RCA inputs ($I forgot) the stock is 3.5mm input in the front. You can select 3 possible gain configurations depending on headphones and how loud your source is. and Free Engraving! (it makes it look less ugly)