TL;DR: ‘Helium’ is a misprint for ‘hellum’ which is a dialect spelling of ‘helm’.
Let’s get the easier parts out of the way before we tackle ‘helium’. The Toad is a “sloop, of 8,825–10,000 registered tonnage”. I don’t really understand this description—a ‘sloop’ is normally a sailing vessel with a single fore-and-aft rigged mast, but a vessel of 10,000 gross register tonnage would be far too large for a single mast—a five-masted clipper might not be so large. Let’s be generous and assume that this discrepancy is a plain hint that the tale is a tall one.
In a sailing vessel, to “sail afore [before] the wind” means to travel downwind, that is, in the same, or similar, direction as the wind. To do so “like a thing of life” means that in this point of sail it responds quickly to the wind and waves, pitching, rolling and yawing like a living thing.
The word ‘helium’ is a misprint (probably arising from an optical character recognition error) for ‘hellum’, as you can see in the Google Books snippet view for the 1973 Doubleday edition of Mitchell’s collection The Crystal Man:
The spelling ‘hellum’ indicates a dialect pronunciation of ‘helm’, meaning the steering gear of the ship, presumably a ship’s wheel in the case of the Toad. There are lots of other dialect spellings in this passage, for example ‘thurowly’ for ‘thoroughly’ and ‘disperidge’ for ‘disparage’. For a ship to ‘mind her helm’ means to be obedient to steering, so that when the steersman turns the wheel the ship turns quickly and without resistance: ‘like a lady’ means ‘gracefully’.