I like your enthusiasm. I doubt that the shop will sit down and show you the ropes to tuning an active setup without paying them. It is pretty time consuming that's why. You can do it at home by yourself for the most part if you do your research but a lot of it is personal preference. It's best to understand what each thing does by actually sitting in your car and listening to it while you change one thing to another. I've never had good luck with auto time alignment so if you decide to use it, use it as a start and go from there. Same applies for Auto EQ. Factory speaker locations are fine but do you have sound deadening inside your doors and seal it up good? That's very crucial to getting the cleanest sound out of your mids. The farther the speakers are away from each other, the more you have to time align and harder to blend. Crossover slopes are pretty important when dealing with active speakers because it will make a speaker sound more narrower/sharp or wider/smooth blending. For tweeter and mid, I would recommend starting at -12db/oct slope to get a good start. If you feel you need to sharpen up the tweeter or something, then move it to -18db or -24db slope for a much sharper sound. It will bring more detail but it will also start to sound more separated the sharper you go. For subs, I usually like to use a -24db slope because otherwise it will sound a little muddy if it plays too high. Crossover points will kinda depend on what equipment you have and how you have everything setup. Ideally you do not want to have a big gap between each speaker so it doesn't sound lacking in one area. For example, if you put your sub lpf to 80 hz @ -24db/oct then put your mids hpf close to there. Move them up and down to see what works best for you. Tweeter hpf can be anywhere from 2.5khz to 4khz depending on your taste and if your tweeters can handle lower frequencies well. Setting your gains for mids and highs individually can be a bit frustrating compared to a passive setup because you can easily make your system sound worse if you don't know what you're doing.
Can you list your equipment here and what other work you have done to your car? speakers, subs, amps, HU, electrical, etc.. How did you set your gains for everything so far?