Make sure you have Glyph of Divine Accuracy and Glyph of Smite active under major glyphs. You'll need both. For the third slot, I like to use the Glyph of Prayer of Mending, mostly because there isn't another choice better than that, anyway.
Your primary glyphs will be whatever makes you feel comfortable playing discipline. You probably want to use the Glyph of Penance, Glyph of Power Word: Shield and the Glyph of Prayer of Healing.
I'm offering an incomplete 31/3/0 spec for you as a baseline to start with. There are seven points left that for you to invest in other talents that you feel can help you or your raid. The extra haste from Darkness is nice and so is the faster Shadowfiend from Veiled Shadows. Or you can go for Strength of Soul, Train of Thought or other holy talents.
Let's look at the cost of Penance. Penance at maximum level will cost me around 2,882 mana (for a dwarf). With five stacks of Evangelism, the cost of Penance drops to 2,017 mana instead. That's pretty darn cheap, if you ask me. This is one of the main benefits that the Atonement spec will net you. You also gain the added benefit of having a pseudo-healing cooldown at your disposal that increases the potency of your spells by 15% and nets you back some mana.
Evangelism stacks can be maintained indefinitely, purely through Holy Fire. What you want to do is cast it whenever it is off cooldown. The rest of the time, just stick to using normal healing spells as the encounter demands. I like to use Power Auras to track when Holy Fire is available. It also helps to create a focus macro so that you don't lose track of your current healing target.
From a positioning standpoint, I like to stay within range of the tank. I figure if I can heal the tank, then that means the boss is close enough that it can be hit with offensive spells, allowing me to refresh and maintain the stack.
Now, should there be any downtime during an encounter where there is little to no healing required, you won't get penalized for casting Smite. When we go up against Lord Rhyolith, I just open up on one of his legs immediately. Periodically through the encounter, I'll hit one to volley my Evangelism stacks up and not lose them. I should be targeting one of those large fire elementals or other adds that spawn, though. They usually die fairly quick before I can get around to them, and there's a ton of raid damage going on as it is.
Just play conservatively and watch your mana bar. If you think you're going to get dangerously low, stop casting Smite and stick to Holy Fire only until you regenerate some mana. You have a Shadowfiend and a Hymn of Hope? Use them!
Great! So when should you activate Archangel? Use it if you know that your Evangelism stacks are about to fall off and you have no hope of maintaining them. If the effect is going to wear off, you may as well make use of the mana return and then gradually rebuild it back from zero.
The other method (which is way better) is if you're anticipating some heavy damage coming on soon. Bust Archangel and go to town while healing every player who is still moving. Cast Power Word: Shield on a player, then follow it up with a Penance and a Prayer of Healing over and over until things become stable again.
Do trinkets matter?
Yes and no. Trinkets by themselves won't exactly make or break your class, but they may alter your playstyle a little bit. Most healers will use some sort of spirit trinket, a mana regen trinket or a throughput trinket.
Those are just some of the trinkets that practically scream "healing" all over them. But I'm going to add two more to that list that just might surprise you.
Wait a minute! Aren't those DPS trinkets?!
Why, yes! Yes, they are! The only offensive spell you'll really be using is Holy Fire. You've got a pretty good shot of proccing both of those trinkets just from the Holy Fire ticks, anyway. If I noticed Theralion's Mirror activating and boosting my mastery (almost over 70%), I'll load up and start casting Power Word: Shield on players around me or cast Prayer of Healing
to force Divine Aegis
through. If I see that my Volcano card has activated, that's an additional 1,600 intellect I'll have temporarily. Resort to actual healing spells, though, to take advantage.
Anyway, you don't need to go out of your way to get those two trinkets. But just keep in mind that you can (and should) take advantage of them when they proc.
Before I close this one out, I want to remind you that I consider this style of play a fairly advanced one. If necessary, test drive your settings at the target dummies. Practice keeping one focused while healing various players around you. Try to get a feel of how much mana it cuts away from you and what else you can do to get it back (or at least, make it mean something).
Spiritual Guidance has the inside line on pre-raid gear, valor point and raid gear, and healing strategies for bosses such as Atramedes and Chimaeron. Newcomer to the priest class? Look into Discipline Priest 101 and Holy Priest 101.