generally, and i mean pretty much always, engineers take the bass directly into the recording unit. no amp. i wouldn't suggest going directly into your computer either, via usb, unless you've got a high-end native sound card inside your machine. if you're just messing around and/or aren't much of an audiophile, you can get away with it. you'll get better results if you invest in an external audio card/ interface, which generally comes with more than one input type/hybrid inputs.
as far as retaining your amp settings, your amp sounds the way it does because of the combination of its physical shape and materials and the voltage flow. this is why bass amps are generally not used in recording. you'd be hard pressed to find a mic or any combination of mics that would competently handle the intake of such low frequencies while at the same time articulating the nuances of your playing. it's far easier to get the track down and then manipulate the quality of sound post recording.
good speakers/monitors are key in finding a decent bass sound as well.
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