We are going to Hawaii next June. One week on the BI and one week on Maui. BI comes first. My question is this: Where do I fly into? Is it better to fly into Honolulu and take an interisl. flight to the BI, or just fly into Kona? Then, when we leave the BI to go to Maui do the interisland people care that we will have all our luggage or is this how it is all the time? Then, at the end of our trip do we fly out of Maui to get back to the mainland or take an interisland flight back to the BI to fly out? What is cheaper, in your experience? I am sure that a travel agent has all of the answers to my questions but I am not patient enough to wait until tomorrow for my answers. Thanks in advance.

Fly direct to Kona if the fare's similar.
Yes, they'll take your luggage on the interisland flights, but there's a limit. If you take too many bags they'll charge you extra.
Fly out of Maui if the fare's similar (doubt that you'll be able to arrange both the Kona and Maui direct flights, though).
You can answer your own question about whether you can do this and the fares by going to Expedia or Orbitz or Travelocity.

Thanks, last time I checked expedia it was too early to check fares for the time I will be there.

If you can get direct flights, go for it. However, depending on where your home base is, JK is right. It is very unlikely you can fly directly in and out of both. There are more direct flights to Mauai than ever before, but many people go through Honolulu and connect on flights that run every hour to the inter-islands - no big deal. Include it in your ticket if you can as opposed to booking direct to Honolulu and booking the inter-island flights separately. It can add on to your costs substantially when two of you are traveling - also, a reason to book directly when possible.

So you guys are saying that it is unlikely that I will be able to fly into and out of either Maui or BI? Or, are you saying that it would be difficult to fly into BI and out of Maui. I think the latter is what you are saying. So lets say that I fly into and out of the BI and just take an interis. flight to maui when needed and back to the BI when we leave. That would work, right? PS we are coming from NY.

Yes, the last scenario you posed is the most likely to work out.
You should be able to check who offers these flights at any of the airline sites (yes, fares may not be available....but check who currently flies into BI and Maui at present).
You'll probably need one interisland flight on the way in or out of Hawaii.

If you can fly direct to Kona, then do it. Then fly out of Kahului, Maui directly home. You can fly into one airport and out of another airport in Hawaii and it is still considered a round-trip(and you don't have to pay the higher one-way fares). So if the airline flies directly to BI you can fly there and then out of Maui. I know both United and TWA fly direct to Kona so only one interisland trip may be necessary - from BI to Maui.