my groups don't often use a designated stronghold.
On the occasions it has happened it is normally just a base of operations, and discussed in the same down time that spells are learned, and magic items purchased or made, ie. "I spend another 1000, on my temple" DM - well thats more than you need for your current shrine in tha back of that noblewomans house, unless you want really expensive furnishings. Its less than a full temple. It could purchase you the land for a larger building and begin on plans." " how bout 2k?" that gets you workers to begin on the foundations - "OK."
The temple in question was eventually abandonded when the party was caught killing a local priest, and had to flee justice in the city.
If the party lives somewhere long enough, and makes enough enemies, eventually someone will attack them there.
I have had one charater establish a new barony, it was mostly disccused over e-mail and run using rules from a dragon magazine- governing trading relationships, road building and other such details.