What you do in encoding really depends on your writing process, which differs for everyone. Plus, most people are still learning Dramatica and how to apply it to their writing, so no one's got it totally figured out.
First, definitely use that Bob Raskoph tool from the other thread to create single-page HTML of the one or two storyforms you like best. They make awesome references. Pretty soon you'll have all the major points memorized.
Next, I'd actually recommend to stop adding anything into the Dramatica application. Now that you have the storyform, I think the rest is best done in a word processing tool. (NOTE: you could skip encoding altogether and just start writing your story now, if you want! Just referencing the storyform when you get stuck or need ideas.)
For storyencoding, start with a very quick pass, where you just write one or two brief phrases for each story point. You can export the Story Engine Settings report, save it to a word processor, and start marking it up like this:
THROUGHLINE: Being the magic-born girl
CONCERN: Having a bleak future
ISSUE: Being prejudged for her devil's blood vs. Openness
PROBLEM: Being a free spirit; Being abandoned by her family
SOLUTION: Allowing oneself to be tamed/controlled [Following the old man's guidance]
SYMPTOM: Making things difficult for oneself; Being chained by rules
RESPONSE: Aiding others (esp. healing)
UNIQUE ABILITY: Accessing the time-slowed dimension / Taking time to calm down and think
CRITICAL FLAW: Outmaneuvering authority
BENCHMARK: Being focused on one's immediate needs (e.g. hunger, tests, escaping execution, avoiding pursuit)
SIGNPOST 1: Being ready (presentable) for the Lord's return home. Also: not being aware of current affairs (recently enacted laws regarding magic-born).
You'll note I erased the original Dramtica terms as I went, to make it feel more creative than those sterile terms. Up to you if you want to leave them in.
If you're not sure on something, leave it blank or throw in a bunch of question marks beside your ideas.