I first want to second doctorcomics in that the most comprehensive way to go about this is to be familiar with the appropriate chapters of House of Hermes: True Lineages and City and Guild.
Once you've looked through those, my question for you, assuming you want to generate a magus/maga (someone else suggested a Redcap Mythic Companion, which would also work well and would be equal in Hermetic social standing), is which of the following best describes your character:
1) A Merchant Who Is Also A Wizard.
My view is this is a merchant child (possibly unaware until apprenticeship that he/she was of the line of Mercere) who had the Gift, and his/her apprenticeship did not fundamentally change the course of the character's life towards mercantilism, just enhanced it.
This character requires Gentle Gift, and in my opinion would be apprenticed quite late - possibly as old as 15-18. Until that point, he would have had secular education and training in merchant skills and professions. I would not take too many Hermetic or Supernatural virtues or flaws; the ones I would take are ones that a young person with magical talent bent towards sea commerce might have or want (faerie blood only of undines or something similarly watery; focuses or restrictions regarding travel or water), and weigh the virtues and flaws more towards those helping in the mundane job.
As for apprenticeship, your character's parens is likely not to be highly specialized in travel and water magic, so before Gauntlet the spells and Arts will be a mixed bag, but once apprenticeship is over, the magus or maga will likely specialize to his/her interest.
2) A Wizard Who Is Also A Merchant.
This character for me would be a result of a bureaucratic decision at Harco; those in charge of House Mercere found they needed another magus or maga to help with the sea trade, so they made sure that one of the current Mercere magi in that field took an apprentice.
Childhood would be covenant-born, but apprenticeship quite early. Might have the Gentle Gift or Inoffensive to (Humans or Animals), but that's a story choice. Virtues and flaws will tend towards the magical; innate virtues and flaws might be more about general magical ability (such as study or lab bonuses, quiet or flexible magic, etc.) than magical foci. Or you could have Mythic Blood and be the child of a Redcap and a sea dragon. Mutantes magic might be interesting; tethering spells to sails, anchors, etc. might be very useful.
Apprenticeship, after basics, will be specialized. While your character will learn the profession and seafaring skills to a decent level, the focus will be on assisting the job magically, so more emphasis on Rego, Auram, Aquam (possibly Creo and Herbam for mending ships) and associated spells.
Post-apprenticeship will be in service to the House. Working on the Mystery of Hermetic Architecture in order to build enchanted sailing ships would be one possible path.
3) A Wizard Who Through Fate Became A Merchant.
This character wasn't really a seafarer, or trained from apprenticeship to take the role. Maybe this Mercere grew up in a covenant that had fishing boats; maybe he/she grew up in a forest and didn't know a boat from a barrel. At some point post-Gauntlet, someone with rank in House Mercere needed to take charge of some of the trading vessels on the Mediterranean and your character got the job (as a reward? As a result of intra-house political ambition? As a punishment? Any work!).
Generate your Mercere however, but don't give him/her too many obvious seafaring skills until after apprenticeship. Hermetic and Supernatural virtues more likely to be incidentally useful to the job (e.g., Elementalist) than something like Minor Magical Focus: Wind.
Because I like giving myself a challenge, I'd make the character a bookworm who expected to be making longevity potions and magical items for Redcaps until, suddenly, at age 28, blammo, out at sea. You don't have to be that radical, though.
Depending on how far out from apprenticeship the character is, the magus/maga could be a remarkably good merchant (at 55, 17+ years of experience refocusing on useful Abilities, Arts, and Spells), but the character would also possibly have more "land useful" spells and abilities from his prior career.
ONE FINAL THOUGHT
If you have Covenants available to you, have you thought about locating your sanctum and laboratory aboard one of your vessels? You might not be able to get the best lab totals, but your character would be able to avoid interrupting lab projects for time at sea.