I'm looking at the XML file now and it uses "BestDefense". Is there a way to make it so it comes up with one for best shield defense, one for best armor defense and one for best point defense?
Yes, simply use values "Shields", "PointDefense", and "Armor". For example, a BluePrint with:
<FillerComponentType>Shields</FillerComponentType>
<FillerComponentType>PointDefense</FillerComponentType>
<FillerComponentType>Armor</FillerComponentType>
Will add your best shields, best PD, and best armor in equal amounts to your ship until it runs out of capacity. Of course, presumably you want to have other components, too... 
The "BestDefense" simply selects the defense component type (Shield/PD/Armor) that has the highest rating. Which is pretty dumb...
i'd rather not reconfigure every time
I hear you. Exactly the reason why I modded the ship blueprints in my game.
My idea of how the ships ought to be probably differ from yours but it's not that hard to mod them provided you only want to mod the ship blueprints as opposed to, for example, creating a new faction with its own ship designs.
The files you need to create under your Mod directory are:
Game\FactionShipStyleSetDefs.xml
Game\Mod_ShipBlueprintDefs.xml
Game\Mod_ShipClassDefs.xml
Text\Mod_ShipClassText.xml
The files prefixed with Mod_* above should contain only your new additional stuff. This is good because then you don't have to care whether Stardock changes the base game files. The file "FactionShipStyleSetDefs.xml" is a copy from the base game version. Here you can't avoid modifying it as you need to add your ShipClasses to those factions that you want to have the new ship designs. When SD makes an update you need to check whether they modified the base game file as you may need to apply the same changes to your modified copy of it. Of course, you can keep this simple by having your ship classes be additional to base game ship classes so that you can just copy&paste yours in case you file is updated.
If you also want to make modifications to the starting ships then you need two more files:
Game\FactionDefs.xml
Game\Mod_StaticShipBlueprintDefs.xml
Again, "Mod_StaticShipBlueprintDefs.xml" contains just your new starting ships while the "FactionDefs.xml" is a copy from the original where you need to edit the starting ships to point to your variants.
One caution, though: If your ships are somehow "special" and need to be used in certain way to make them effective then it's probably better to not have them available for the AI factions, because the AI probably wouldn't use them as you intended them to be used. Alternatively, plan the designs so that they are "uncomplicated" so that the AI doesn't need to understand anything else than just building them and pointing them towards an enemy.
Also, the <Role> tag in the blueprints doesn't work. Or, at least, didn't work in v1.1. Haven't been paying attention in the current v1.2. whether they have fixed this. Probably not, though...
