Tokyo to Akita, then Akita to Kyoto?

Hi guys, I was wondering if you could help me. I'm not very smart, so I'm a little confused on how I'm going to make this trip work out...
I'm going to be living at a university in Akita in the Spring(April). I have to land in Tokyo at around 5, then take the Komachi train to Akita that evening. I'm hoping the Bullet trains are right by the airport. Then after the semester is over, I want to go from Akita to Kyoto for a couple days, then back to Tokyo, where I will fly back out in August.
The thing I'm confused about is that I don't see a schedule for the bullet trains. I'm scared that when I arrive and get my ticket, I'll have to wait 8 hours or something. Plus, I don't know how to make seat reservations, and don't know how to Kyoto from Akita. Can anyone give me peace of mind! I really would appreciate it!! I've never done this before, and am going by myself, so I'm scared to death.

I have to land in Tokyo at around 5, then take the Komachi train to Akita that evening.

What airport are you arriving at? Haneda or Narita? If you arrive at Haneda you may want to consider flying to Akita instead of taking trains. It will be both faster and cheaper.

I'm hoping the Bullet trains are right by the airport.

They are not. But there is a fairly easy train connections to the nearest shinkansen stations.

Then after the semester is over, I want to go from Akita to Kyoto for a couple days, then back to Tokyo

Again flying will be much faster, and may be cheaper if you can get a discount flight. See this page for Akita transport options:

http://www.japan-guide.com/e/e3626.html

The thing I'm confused about is that I don't see a schedule for the bullet trains.

Hyperdia is the go to site for train schedules:

http://www.hyperdia.com

I'm scared that when I arrive and get my ticket, I'll have to wait 8 hours or something.

Don't worry, the trains leave hourly.

Plus, I don't know how to make seat reservations

You make them when you purchase your ticket. You will be asked if you want a seat reservation and what type of seat (aisle/window/middle) you want whether you your ticket from a ticket machine or from a ticket counter.

I've never done this before, and am going by myself, so I'm scared to death.

Don't worry, you'll be fine. Have a good trip!

Thanks for your prompt answer! I have to admit, you scared me a little bit when you said the trains aren't by the airport. I think I will be arriving from Narita? I will be purchasing the plane tickets this weekend, but I'm pretty positive it's going to wind up being Narita.
As far as flying from Tokyo to Akita, I think I am making a mistake on the booking of my flight or something, because the price fora plane ticket from America to Akita airport is practically 3 grand compared to just going to Tokyo for 1800 :/. Plus I'm scared I will miss my flight to get to Akita from being lost...lol it sounds really intimidating

I have to admit, you scared me a little bit when you said the trains aren't by the airport.

Just to be clear. There are easy train connections to both Haneda and Narita, just not the high speed bullet trains.

I think I will be arriving from Narita?

Then you will need to travel to Tokyo to catch the train to Akita. The Narita Express (approx 1 hr) is probably the easiest. See here for more info.

http://www.japan-guide.com/e/e2027.html

I will be purchasing the plane tickets this weekend, but I'm pretty positive it's going to wind up being Narita.

Depending on where you are coming from, Narita may be your only choice.

As far as flying from Tokyo to Akita, I think I am making a mistake on the booking of my flight or something, because the price fora plane ticket from America to Akita airport is practically 3 grand compared to just going to Tokyo for 1800 :/.

Have you looked into discount air tickets? They can get you really cheap domestic flights in conjunction with your international flight.

http://www.japan-guide.com/e/e2364.html

Otherwise consider booking each leg separately to get the best deals. Note that flights to Akita depart from Haneda Airport, so don't forget that you will need to transfer between Narita and Haneda. Bus (90 min) or train (105 min) are best for that.

Plus I'm scared I will miss my flight to get to Akita from being lost...lol it sounds really intimidating

Don't worry, its not too bad. Just plan in extra time to make your transfer just in case it takes you awhile to get your bearings upon landing. Or consider staying the night in Tokyo and taking the flight/train to Akita the next day.

Thank you! Just got the ticket and it is definitely Narita. Thanks for the tips. Also, just out of curiosity, I've wondered if the shinkansen is 24 hour service? Someone told me a horror story about how they were trapped in the station overnight. I'd hate to have to go through that!