It doesn't. Move it out of checking somewhere else - like an envelope.

Loan-to-self makes perfect sense, even in double accounting systems. Just move money from an asset to a liability. After all a negative liability is an asset. The only issue is physically moving the money somewhere (e.g. from checking or savings into an envelope).

I presume it's a liability account setup separately from assets.

GnuCash can easily be used with 'The Cloud' as well - for example, keeping Gnucash files and settings (e.g. reports) on dropbox is trivially easy. Security is a concern with any cloud based approach and represents a tradeoff IMHO, albeit one that can be mitigated (e.g. cloud encryption).

One per credit card, but I think either way would work.

Um yep - strange. For what it's worth, as soon as you click to edit, the decimal value is displayed for editing. But still, I'm yet to see a broker report prices in that format. I'm guessing somebody went rogue on this one. Posted to gnucash-users - if an answer is to be had, it will be had there relatively quickly.

Might also want to consider everything over to a single broker (e.g. Fidelity, Vanguard, etc) as you'll likely have many 401ks in the future and it's easier to manage them when they are consolidated.