I suppose the days you go is just a personal preference...but I've heard that first of all, airlines are least busy on Tuesday, Wednesday & Saturday (not sure if I believe the Saturday part!). The hotel rates are usually higher on the weekends and includes Fridays usually. I typically plan our vacation from a weekday to a weekday...like Tuesday to Tuesday. This saves you money on airfare & hotel rates. Plus the parks & Downtown Disney are busier on the weekends.
You can go on Disney's website & create an account for yourself. You are able to create up to 5 vacations & can compare the costs that way. If you have more questions on how to do this, please feel free to contact me! I planned my first vacation last year myself so I completely understand how overwhelming it can be! You have taken a great step with reading the DISboards...I wish I knew about this site last year! It would have helped me tremendously!!!
You said you are getting 4 day tickets...I do not recommend park-hopper with young children. My parents insist they are the greatest thing since sliced bread...I do not. I enjoy going to one park a day & taking our time walking around, enjoying the rides/shows, eating/shopping, etc. Between all the rides/shows, the parade, eating, the fireworks...I don't see a need to go to more than 1 park a day. (I also think your children are probably too young to enjoy the waterparks, so I would skip the "water park" option as well) If you do not want Park Hopper or Water Park, you just need the 4-day Base Tickets. (its also very convenient because if you stay on Disney Property, they give you a "key" to unlock your resort room (looks like a credit card) and this card can also be used to purchase items at the parks (automatically charged to the credit card you gave the resort) AND this card is also your park ticket!)
For young kids I would say DEFINITELY go to the Magic Kingdom...it just isn't a complete Disney experience without the MK. We went last year with our 10 month old & didn't go to Hollywood Studios because I thought it would just be a waste of money. I came home & researched the park & cannot believe we didn't go! HS has Playhouse Disney, tons of characters that smaller children know from tv or movies, Toy Story Mania, Honey I Shrunk the Kids Movie Set Adventure (play area -- 11,000 sq ft!!!), Little Mermaid, & many others! I was there years ago when it was still MGM & just remembered it was geared more towards adults or teens...but I definitely recommend Hollywood Studios for your trip! I also suggest eating at the Sci-Fi Diner (your table is actually a 1950's car) and the Character Meal at Hollywood & Vine...while I haven't been to either myself, I have tons of friends/family who have & they recommend both!
In my personal opinion, if you are getting 4 day passes, go to 1 park each day...then you will be able to go to all of them. However, you can always change this once you get there. For example, if your kids love MK, you might want to spend 2 days there & skip another park (IMO I would skip Animal Kingdom if you are skipping one).
If you stay on Disney Property, you get free transporation to the parks & to other Disney resorts (via bus, monorail, or boat). I didn't know this last year, but you can eat at ANY of the resorts...just ask at the front desk & they can tell you how to get there (usually by bus). We never waited more than 10-15 minutes for a bus. This is VERY convenient. You don't have to worry about parking in the lot, paying for parking, remembering where your car is, walking long distance, etc. They basically drop you off right at the gate of the park (GREAT for travelling with kids!)
My best tip with children...well actually 2 tips...first of all, each park has a Baby Care Center...they are WONDERFUL. I appreciated those, as a mother, more than anything else. Don't let the name fool you...they aren't just for infants. They have changing rooms (loved the one at MK the best), a play room, private nursing rooms, rocking chairs, etc. They are also airconditioned. I needed Pedialite for my son on the trip & this is where I got it! My other tip is to take a break in the middle of the day for naps & refreshing! This is a MUST with children. The parks can be overwhelming for adults & definitely for younger kids. This is what we did...we would arrive at the parks early in the morning (usually by 9 or 9:30) stay until after the parade (usually between 2-3:30pm) and then take the bus back to the resort. It usually takes about 10-20 minutes to get back to your resort depending on where you are staying & what park you are at. We would either use the resort pool, get something to eat, or just relax in our room (while the baby napped) for a few hours. Then we'd go back to the parks around 6:30 or 7 and stay for the fireworks. (This of course depends on your schedule & what time your kids nap & what their bedtime is.)
About making reservations...as I said, we are going in late November & I actually booked the resort & park tickets last week. I'm waiting on airfare (most don't have flight data out yet) until probably mid-May or June. If you book now & get a discount code or a better deal comes along, you are able to call Disney & make changes. You can also change your dates if you need to. You can make dining reservations around May or June (90 days prior to your vacation). I highly suggest doing this. I like to just "go with the flow" on vacation...I don't like having to be certain places at certain times. However, if you don't plan your meals ahead of time, you won't get to eat at your chosen places. Last year we were at Epcot & luckily got into Coral Reef right as they opened. We only waited about 20 minutes. Right after we sat down, I got up to use the restroom (this was 11:30am) & overheard the CM at the front desk tell a lady she wouldn't be able to get in until at least 5:30 or 6pm because they were FULL all day long! This is why I am making ADR's (Advanced Dining Reservations) as soon as my 90 day mark hits!
I apologize...you said you were overwhelmed & I just gave you a ton of information. Since you are going in November (as I am) please feel free to contact me with any questions you have! I have learned a ton from being there, reading DIS-posts, using the Disney website, and from friends who work down at Disney!