That's a hell of a good Xmas gift if I do say so myself. Taking the time to set it up correctly the first time is a smart move and will pay off for you.
First off you must accept the fact that there will be a learning curve with CNC Machines unless you have previous experience. That said, I started with zero experience and learned by watching a few You Tube videos but mostly from reading this forum. The users here are almost always quick to answer your questions. Just remember to provide as much detail as you can when you post your questions to enable the users to give clear answers. To save time, search the forum for questions and you will usually find the answers without ever having to ask.
Next, you won't be using Mach3 unless you completely modify your system. Mach3 uses a different circuit board to control the machine and it is not offered as an option by Inventables. You can use Easel, which is a combination of software packages all rolled into one. With Easel you can design your project, it will generate the required G-Code, and send it to you machine to carve. There are other and more powerful programs out there that you can use to design your projects and create your g-code files. The other design programs you usually generate the necessary G-Code and you can sometimes import that code to Easel for carving buy usually you will need another program to send the code to you machine to carve. Other programs for sending g-code to your machine for carving that are popular are Universal G-Code Sender, (UGS), which is free but it does suffer from some issues. For the most part it works fine but if you are going to do a large 3D carving then it will often freeze up during the carve. Then there is my personal favorite PicSender, It cost right at $20.00 but does not suffer from drawbacks of UGS and has a more user friendly layout.
As for storing the stepper calibration, there are some settings in GRBL which is basically some software that is part of your machine. The settings store several different things and among them are the stepper settings. Those are stored in a line of code that on your machine that configures how many steps are required to move your machine in a particular axis 1 mm. Your machine will come with default settings which will be very close but not always dead accurate. Stepper calibration checks this accuracy. Depending on the type of carving you are doing the default settings may be "close enough". I personally don't like "close enough" and much prefer my machine to be as accurate in ever aspect that I can control. There are several methods and spreadsheets available to calibrate your stepper motors. Once you have done the calibrations and determined the exact setting to use, you then update your settings and they will remain intact as you use different software programs to carve your projects. My video tutorial walks you through it step by step. It's much easier to do than you think and once you have it done then you won't have to fool with it again for a while. As your machine ages and belts stretch or get adjusted you may need to recalibrate. For more info and other opinions on how to do it just do a forum search for stepper calibration.