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Hi Justin,
Welcome to Iceinspace, good to see another person getting into this hobby. You never know one day in the future you may be the first person in the world to see a new comet and have it named after you.
As far as software goes, you can download Deep Sky Stacker which is free and is a good starting point. Also there are quite a few try before you buy software packages around such as Nebulosity, Astroart, Backyard EOS and APT.
As you have a FUJI camera finding the software that supports your camera's RAW image will be your first task as most of these astronomy software packages are Canon biased when it comes to DSLR's. Otherwise you will have to save your images as Jpegs which is not as detailed, Jpegs are 8bit, RAW is 12, 14 or 16 bit (depending on the camera).
To get sharper detail you need accurate focusing and there are masks that can go over the front the telescope to help you with this, such as a Bahtinov mask or the Hartman mask which is very easy to make yourself. Put the mask on, get the focus perfect and then take it off.
Polar alignment is only for accurate tracking and does not effect Goto unless your polar alignment is completely way off.
Goto only needs 2 alignment stars to be centered on your camera. Your GEM6 handset will prompt you with star names to point at, to get this alignment correct. Grab a copy of the free Stellarium software to help with the location of the stars that the handset asks you to align with. The handset will give you a choice of a dozen alignment stars in case some are blocked by trees etc.
May I suggest go onto YouTube and look up Astronomy Shed, Dion has made a whole series of tutorials for first time astronomers starting out. These videos helped me out a lot when I first started and he provides a lot of useful information, he even shows you how to track and video the international space station with a webcam when it passes overhead.
Hope this helps,
Regards
Bill
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