To be honest I think it's a bit too early to say right now. On the PTR even in heroics tanks are getting beaten up pretty hard, as they scaled up monster damage output, so the numbers will probably get rebalanced a bit before the patch goes live.
The biggest thing to get your head around right now is the revamped system of every healer having the three base heals - the slow, small efficient heal, the slow large heal, and the fast inefficient heal. They apparently expect healers to use the slow small heal when there is not much else to do, and to balance the other heals with their cooldowns during heavier damage.
Also, right now I'd pay more attention to what Blizzard says about healing than what the experience is like on the PTR. Here are some recent examples:
The reason I say to watch what they say more than what they do is, they've been very clear that if the PTR behavior doesn't match what they have in mind, they'll tweak the numbers until it does. In the last PTR patch most healers just spammed their slow, efficient spell because it was getting the job done... so in the next patch Blizzard nerfed those spells, as they want them to be only a fallback and not strong enough to stand alone. That sort of thing may well happen once or twice more before the patch goes live.
Incidentally, I find that checking the top page of mmo-champion to be the easiest way to keep track of Blizzard's position on things.
The "five second rule" no longer exists in Cataclysm. You have a fixed rate of mana regeneration while in combat, and another fixed rate of mana regeneration while out of combat.
Out of combat
Your out-of-combat mana regeneration rate is based on your spirit. "Mana per 5 seconds" (MP5) no longer exists on items, and has been replaced by spirit. (You'll still see it on mana oil, though.) Every class that has a mana bar will regenerate mana this way while out of combat.
In combat
All classes start with a baseline regen rate of 5% of your base mana per second. (Base mana is the amount of mana you would have with 0 intellect.) Classes using healing talent specs gain a passive ability called Meditation, which lets half of your out-of-combat regeneration continue while in combat.
For non-healing specs such as mages, warlocks, and shadow priests, spirit does absolutely nothing for your combat regen. Many talents and abilities exist that give you bonus mana in combat, however: Replenishment, Archangel, Hymn of Hope, Shadowfiend, etc. Mages can passively regenerate mana using Mage Armor.
Best Answer
It is only the presence of your Holy Fire that determines whether or not the glyph's bonus damage applies or not, similar to any number of other symbiotic spells in WoW.
That said though, Holy Fire has a higher damage per cast time than Smite, so there's no reason why you'd ever cast Smite when Holy Fire is off cooldown and its DoT is off, making your question kind of moot.
Some numbers to show you what I mean visually: