Where you've defined the <entity> itself, you set up the bootstraps within the entity. Here's an example from Pathfinder of the entity used in the -Custom/Magic Weapon-:
Code:
<entity
id="gMagWeapon"
form="MagWeapon">
<bootstrap thing="gCustMagic">
<autotag group="Helper" tag="MgMult2000"/>
</bootstrap>
<bootstrap thing="LegItemHlp"/>
</entity>