I currently have my magni hooked up to the output on my motherboard. The motherboard is a Z87E-ITX which has a TI NE5532 Premium Headset Amplifier onboard. Am I double amplying my signal and is this a decent setup till I get a modi or another dac? I am using this with some HE-400.
Yes, and Maybe.
As long as you try not to overdrive the Magni, it's probably decent enough to listen to temporarily. The thing I always worry about in a setup like that is, the input to the Magni really isn't designed to handle a high input level - it's designed for a "line out" from a DAC. So basically it is possible to drive the Magni harder than normal with such an arrangement. How much is too hard? That I don't know. I also don't know what will happen to your warranty if you blow a Magni by over-driving it (nor do I know if that's possible).
I do know that I've used my Magni with two different DAC's. One has a 1.5 volt output (the Schiit Modi), the other a 2 volt output (the Pure i-20). The device with 2 volts output drove the Magni a lot harder and made it run much hotter.
What I think I would do is, turn the Magni volume control to about noon (or a bit higher), then slowly increase the volume control coming out of the computer until you're at a moderate listening level. Then, use the Magni volume control to fine tune the listening level. If your Magni gets hot, turn down the volume of the computer.
I would not listen to that setup permanently. You'll notice a distinct difference when you start using a DAC.