Spells are easily altered or re-written to be new ones. I never have more than half my complement of spells from the books, I always invent new ones. I simply add one of the correct Te&Fo and alter anything not fitting, like base level, R/D/T and so on. Easy as pie...mmmmmm...pie....
V&F? Yes and no. You can choose 'Generic Minor/Major Virtue/Flaw' and give it a name. But I still am not completely fluent, so I can't rell you how much it can be customized, if you choose V&Fs that directly affect other totals. But good fields for notes, so you can write down a 'remember this' note.
Example: If you have house rules about how Deficincies work, and still run them like 4th ed versions, where the Deficient Art alone is halved, not all totals.
Abilities are easy to custimize, by writing new ones. Also you can alter any set bonus to them (like for puissance, which the system automatically adds). I made a heroic faerie based companion, who had a Virtue stronger than Strong Faerie Blood (Faerie Leagcy IIRC). Having 'Dwarf Blood', the system grants you a +1 to all Craft skills. But Legacy raised this to +3 in one field. So I could change this particular speciality to be a +3 rather than a +1.
Combat totals can easily be altered, with positive or negative modifiers, you simply alter the Weapon Stats the program finds in a database for this particular entry on the Equipment sheet. I'll wager you're thinking about Weapon & Armour Quality?
I also find the Enchanted Device Creator very good. I was inputting a Redcap, who has a few devices. You simply choose Te&Fo and can then call up the guidelines for this, pick one, and then modify R/D/T, uses/day, Penetration etc.
Having inputted non-starting characters - i just made the raw input for them as they were. But since then I've been using the Advance options, and input what book they read, what ability they train, what they get exposure with and so on. This generates a log to keep tabs on what you do. I still keep my own log though, since I sometimes need more information.
