I have the bass guitar plugged into the SD50, and I had created a MIDI drum track. But when I record the Bass Audio it records the audio from the MIDI drum track on top of the Bass Audio track. Any ideas? I know it is probably really simple. I have started to write down my configuration which I forget to do each time.
 
Sonar LE 8.5

You didn't mention what sound card/audio interface you're using.
Whatever that is, make sure that Stereo Mix or WhatUHear is not on. It might be called something else on your sound card. This is an input setting that records everything you hear.

oland SD-50 Sound Canvas

Roland and Cakewalk teamed up to create an awesome, portable sound module and interface called the SD-50 Mobile Studio Canvas. The SD-50 gives you a musical multi-tool that can handle anything from simple 2-track recording or playback, to being the centerpiece of a live, one-man-band. It offers you high-quality XLR and instrument inputs along with onboard effects, and the SD-50 Mobile Studio Canvas can play your backing tracks from a USB flash memory drive while providing you with a fully multi-timbral sound engine for your keyboard controller. No matter what kind of music you create, the SD-50 Mobile Studio Canvas has tools that let you do more. 
 

So my guess is your playing back a complete mix through the stereo outputs of your SD 50. 
I'm also guessing is you posted here because they included X1LE with the SD 50. 
You have the option of using the SD50 as a stand alone recorder, or hooking it to your computer and use it as an audio interface and record directly into Sonar. 
Or I guess a combination of both. 
You'll have to decide which way you are comfortable with. If you use the SD50 as a stand alone recorder you are very limited with editing. Myself I would dive in and learn how to use Sonar. 

Yes Cactus is correct, Roland SD50 as per the subject line.
 
I have had this working before so I am not sure what I haven't set this time.
 
I should be able to only record the bass and not have the audio from the MIDI track repeat through. I'm just not sure what to switch to get this to happen.
 
Andrew