A lot is going to depend on the configuration of the plane that you are on from smallest to largest you have
1 aisle 2 ( I would sit 2 and 2 with a kid at the window and adult on the aisle in rows right in front of each other)
2 aisle 2 ( you could do the same or sit with adults across the aisle from each other)
2 aisle 3 ( either sit on the 2 side in 2 rows in front of the other or sit 3 in one row and the 2nd adult either across the aisle or in front or behind. Not if both kids are in carseats no one even the parent can sit between them or at the window)
3 aisle 3 ( one row and either across the aisle or one behind or in front)
2 aisle 4 or 5 aisle 2 (either 2 and 2 in front of each other or sit 4 in a row in the center section-since there is an aisle on both sides it does not matter if there is a carseat in the middle though I don't think you can sit aisle, adult, carseat, adult, carseat either aisle or another person because the adult between the carseats could be trapped between them, but you can sit adult car seat car seat adult.
As far as where it depends on the type of plane for the CRJ series I find it easiest to be in rows 3-5 or just behind the wing. Row 1 you have no under seat storage and row 10 on back ( if it has 18 they are a long plane on these) tend to be a lot more rough if there is turbulance so avoid there plus with kids you can't be in the emergency exit ( window style) or the row in front or back with usually at row 7-9 depending on the total number of rows in the plane.
737, 747, or 757 series as long as your not more than half way between the wing and the back of the plane your good, since these tend to have the level between economy and first class there is few if any rows in front of the wing for economy, usually there is an emergency exit (typically a door) over the wing). The problem is visibility for seeing anything other than the wing and some clouds is limited at best though since you kids are so young it might not matter as much to you. Mine at 9 and almost 12 it can be a problem especially for the younger one)
Airbus typically the same but since these usually have 2 aisle I would consider the middle section with an aisle on either side.
Sitting more than half way between the wing and the back can mean that you will feel turbulance more as well as the engines under you which are not conducive to sleeping for some people if it is a long flight especially if it is early in the morning or late at night.
I have found
www.seatguru.com to be fairly accurate to give me a general idea on seats though the ones with comments be sure and read ( obviously if your under 5'5" and someone over 6' says there is no leg room on a seat it's not going to matter as much to you).
Since SW does not service my area ( not driving 10 plus hours each way depending on which airport I would use that does) I don't know much about them but I do understand that your boarding group depends on when you check in online and that families who do not get in group A are boarded between groups A and B.
Most airlines will allow you to have one adult board when your group or section is called to set up a carseat with the other adult bringing the kids at a later time so that they are not standing in the aisle waiting for the seat to be installed or trying to fight it.
http://flyingwithchildren.blogspot.com/
This article has lots of tips on anything you could ever imagine and then some on flying with children. The author is a former flight attendant and has also traveled extensively including to many different countries with her own children both as the solo parent traveling and as a family so things are from both the perspective of a travel professional and a parent ( there is a great section on diaper changes on a plane if necessary that does not involve lugging a huge diaper bag to that tiny lavoratory)
