To include the deed bonus for the attack, click the star icon (in the weapon list or weapon detail). You need to click the ‘Deed’ button each round to set the attack/damage bonus. If you need to manually adjust it for any reason, you can edit the ‘Result’ field in the ‘Weapon Meta’ window accessed by clicking the magnifying glass to the far right of the ‘Weapons’ header.
First priority for spells is to set up the actions for each spell, including the cast action, so players don’t have to fuss with duplicates, etc. I haven’t used Crawlers Companion for a long time - do you mean roll a spell check and have the table result display (without manual lookup)? I will figure out a solution for that because it seems like something the ruleset needs to do, but I want to keep the roll linked to the character sheet rather than a separate rollable table.
Spellburn is tricky. I do think the character sheet needs a way to track temporary ability loss, including spellburn and luck, so that will be there at some point. Currently, the actual bonus should be added to the modifier box, and the ability loss added as an effect to the combat tracker (by the judge) - ‘Spellburn; AGI:-3’ for example.

