This is a very big topic and outside the scope of a single post. But I'll try to keep it short.
Basically, a temple's holder depends on your faith. Theocratic rule = the realm priest of the title holder of the county holds it, lay clergy = you can hold it yourself, or give it to anyone like you would do with a city. Those small title holders have the rank of baron, and the small titles are baronies. To my knowledge, lay clergy holders are taxed like feudal vassals, which is why theocratic rule is considered superior.
Theocratic rule allows you to get 50% money and 100% levies from temple holdings just by having +100 opinion with your realm priest (with 0% of both if he doesn't like you at all). It's easy money from those holdings and it doesn't count towards your own domain limit, so you can get a good amount of money/levies from it just by having good relations with one single person in your court.
Cities are republic vassals and they fulfill republic obligations, which is different from feudal obligations. One major difference is that republic contracts are fixed and can never be changed.
The question is, are they good? I'd say yes. We had a discussion here about it a month earlier, the short of it is that you can build a realm entirely of republic vassals and become obscenely rich by doing so. Such a realm is incredibly stable (as republic succession knows no partition), offers huge development and a tax income that is worlds apart from what you can ever get with feudal vassals. We're talking about a tax contribution of 70-100%. But it requires you to invest dynasty legacies, traditions and innovations to make it work, of course.
Anyway, the normal republic barony contributes 20% tax, which is double the base contribution of feudal vassals (10% at normal rate, 25% at extortionate). Cities are worth it, though not enough for you to construct buildings in them. That's only useful if you want to correct mistakes (i.e. overwriting buildings like barracks, to raise the taxable income of the holding). The same for temple holdings, it's only worth it if you have too much money, so you can build things in holdings of your vassals.
As to your last question, what is better, spreading out or having as many baronies in a county as possible? I'd say it depends. One factor is that only county capitals have 4 buildings slots, baronies in those counties usually have 3 slots. That one extra building alone doesn't make a huge difference, but if we're talking about 10 counties? That means having or not having the additional income of those 10 slots/buildings.
Also, personally holding as many counties as possible means that all those baronies are your direct vassals (they don't count towards your vassal limit, btw), so you get their tax at the normal rate. For a city that means 20% tax, instead of 2% if they were your indirect vassal (10% feudal tax from those 20% republic tax). Cutting out the middle-man in as many counties as possible is profitable.
When is it worth it? When you're facing problems with managing your succession. It's easier to keep a few counties together, baronies can be revoked without tyranny, after all. Many counties are harder to manage with partition. County titles can't have elective succession, so it can become a problem if you have several eligible heirs.
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