I've used PCGen for purposes like these in the past, and while I found the program a little slow it otherwise did the job just fine.
I usually keep a small notebook with stats written in them, like a monster stat block.
I find it better and faster than digital resources at the table.
It really depends on your familiarity with the game system. Like you, I'm at the point at which I'm comfortable free-handing statblocks of any level of complexity, but getting there took a lot of practice. Using a program can be really helpful when you're still learning. You can always print out the statblocks when you're done.
There's also class templates in Unchained I think.
I'm more interested in something that does all the tally work for me.
I mean, right now, I'm looking at a Wyrm Red Dragon with the Grave Knight Template and a yet-to-be-determined number of Anti-Paladin levels as the final boss for the campaign. A program that would start with the creature type, adjust for the template, then allow for addition of character levels, all while keeping appropriate track of statistic adjustments, new feats, skill points, class abilities, etc., and then print them out in a relatively concise single document is what I hope for.
I'm trying to avoid having to look in multiple different places to get all the abilities for the creature at game time, and writing/typing all of it down is a pain in the butt.
This will be magnified as I'm working backwards in the campaign, starting with the boss, and then creating his supporting cast, which I also plan to have similar, though lower powered, builds.
Coupla things:
1) A graveknight template would actually not be that great on a dragon, given the jump down from d12 racial HD to d8 racial HD. Paizo doesn't have a good fix for this since the Dracolich I believe is closed content. You may find the template makes you weaker.
2) Adding class levels to dragons should improve on their already existing abilities. Since they cast as a sorcerer, the forums here tell me that advancing them with levels of sorcerer improves their already existing CL, stacking like a prestige class. You could level dip fighter and even go Eldritch Knight after to advance BAB progression as well, if you don't care about the bloodline. I believe red dragons can also cast cleric spells as arcane spells, so something like a house ruled opposite of Bestow Grace of the champion might give you what you need, without making a monstrosity.
As far as your progress goes, you're doing it right. You always want to know what the boss monster brings to the table so the minions can fill the gaps in accordingly.