Honestly I think you would have been better off getting a machine such as the 1015 model as it is more versatile when it comes to using other software for design and cut. If you are going to use a 1013 you would have to have some design and cut software and also would need a post processor for the code, to slow down the table movement ( Y axis ) because it is gear driven and not designed to move very fast. I have not used any software other what came with the machine myself, there are however some other posts on here that relate using other software and the post processors that are needed to slow down the Y movement. Most of the posts that have some good info are by member Greg.
You did receive the ipicture software disk with the machine I hope. While it is possible to manipulate pictures to give you gears and such, it would take some trial and error to get the gears exactly as you want them. I'd try scanning your cutouts into a picture format, then enter that into the software and cut at a very shallow depth. Then take a scroll saw and cut the gear out following the pattern. That would give you a gear, and playing with the sizes might give you what you want.....but it sounds like an awful lot of work to me (then again, I'm lazy). It would be easier to just put the pattern on contact paper and cut it directly with the scroll saw.
As far as straight lines, if you just want something along the x axis line it would be reasonably easy to draw a line in Publisher or some similar software, and then save it as a .jpeg or .png file and have ipicture cut it out for you. In publisher you could manipulate the width of the line, and through trial and error the 1013 can cut it into your board the way you want it to.