Without knowing level or resources available, it's hard to answer this.
But one of the first things I'd do is make Simacrulums of the royal family to handle day to day basics that don't require the real family. Basic speeches, parading about and visiting the people, and so on. When transporting the royal family, the fake versions would go about in the official carriage while the real ones are teleported to the new location inside a portable hole. Furthermore, I'd hide the real names of the family, using the official names only for the Simacrulums. Thus, divination spells target the fake ones and get them killed first.
I'd also use Improved Arcane Lock on all important areas of the castle, so that only certain people could walk into restricted areas... this will keep out most skillmonkeys (as Open Lock simply fails against that spell). Choke points would lead into the high security areas of the castle, guarded by Permanent Alarm along with Improved Arcane Lock and mundane defenses like soft squishy floors that clearly show when an invisible person walks on them. Permanent Phase Door is worth considering too... put the actual guards guarding a real door, behind which is a ton of nasty traps (ghoul glyphs over water filled pits are amazing for defenses), while the Phase Door to the side is where people actually want to go. Most likely the actual secure areas (where the royal family are, the treasure is, strategic points, etc) will only be accessible through a few passages, and will either be deep underground or connected by portals from far away. Perhaps a portal set into a hole of hiding is the real way to the actual chambers.
JaronK