I assume that since you have done your second racking the fermentation is completely finished. If you still see air bubbles with the air lock on the carboy either the fermentation hasn't fully completed or you have some CO2 gas in your wine. Assuming that the fermentation is complete, did you add any sulfite to the carboy? If not you will want to so that you can protect the wine from oxidation and bacteria. You should be ok for a few days with the carboy not fully topped off. I think you will find that the smaller bottle will clear substantially in a few days, then you can top off the carboy. If not you will need to bring the wine level up in the carboy. To do this you can either top off with a store bought wine of similar variety or I have heard of people using glass marbles to bring the level up. If you use marbles make sure they are glass and you sanitze them.
As for the smaller bottle, I would transfer it to an even smaller bottle as you have a lot of exposure to air with that much head space.