Well, I like to call and do it directly through Disney. I find it easier, and I like to control my own reservation whereas if you use an agent, they own your reservation, so you have to go through them for any changes.
I like to book a package. We book room, dining, and tickets all at once, then we wait for a pin or a special for free dining and shift our dates if we need to. If you have an idea of when you want to go...well, let me just give you a scenario to make it easier: Say you want to go in October. You book and then they announce that free dining will be offered for the month of September all the way through the 30th. As long as you book one of your days during the free dining special time period, the rest of your trip will have free dining as well. This actually happened to us this year. We were booked in October, so we just shifted our dates to September 27th for arrival and departure being on the 7th of October. We have free dining from the 27th through the 7th b/c our arrival day landed within the free dining dates. Hopefully that was easily understood! I would have a couple backup plans for dates just in case. Here is a link to the historical discount dates for when specials and pins have been released in the past:
http://www.mousesavers.com/historicalwdwdiscounts.html
As for flights, it is really up to you. We've done both. I sometimes play with Disney's booking feature on their website to see what the flight prices would be if I booked them through Disney. They are comparable/the same as if I were to do it myself. The only difference being that I would have to pay for the flights up front doing it that way. I would rather find my own and pay for them after I save the money. I just go directly to the different airline sites and look up the flights. I find that there are more options that way. When we have the money all saved up, we will book through the airline and then give Disney our flight info for Magical express. That way they know our arrival time as well, and our room has always been ready. That is not guaranteed of course, but between them knowing our arrival time and using online check-in 10 days in advance, our room has always been ready.
As for pins with packages and such, it really depends on what would be the biggest discount for your family. I would encourage you to play with the booking feature to get to know the different ways you could book and what everything would cost. I love free dining, so I will often plug in a room and tickets package and leave off the dining plan so I can see how much it would be with free dining. Sometimes I will plug in the room only and figure out how much the discount would be off of just the cost of the room. Free dining always wins out for our family, but some people save more on the room. We have to get two rooms for 7 people in our family, and for our extended family we need one more room. Free dining saves us thousands.
Some people are going to suggest staying offsite b/c of the savings, but we love staying onsite. You just have to decide what works for you. We love doing all the table service restaurants and think of them as part of the whole Disney experience. That is just how we roll though. Some people don't care about that. I figure, if it's free it's for me.