First of all decide which of the magic varieties you want your scenario to include. For me personally that means "personal" magic and divine magic, but not sorcery which is anathema. That's not to say it might not come up at some point, but if it ever does every other person in the world will decry and shun them. At some point I will also include spirit magic and potentially blood magic (though again that will be looked upon as evil). Your choices will depend on what sort of fantasy game you are running.
Secondly, make sure your players have a good idea of the sort of game they are playing in so they can make certain choices in character generation. Much like any RPG, including Traveller, you don't want them all making characters who can barely swim and have no proficiency with boats when the game is set on archipelagos.
The d100 system is pretty basic. Roll under the skill to succeed. Get 10% or under of your skill for a critical success (ie 01-07 if skil is 70) and a 99-100 is a fumble (that range can be increased depending). If it's a vs roll and both people succeed then whoever succeeds by the most on their roll wins (ie rolls 12 when needing under 30 wins over rolls 27 needing under 32). You call call that degrees of success like in other games.
Run a game You like primarily, but think about what your players will like too and add that into the mix. Use their personal stories and background to throw things at them that they are both good and bad at.
There's lots more advice I could give, but it really depends on the sort of advice you want. You may already know some or all of the above because you've GMed before. I could be preaching to the converted for all I know. Let us know what you would like advice on.
Sam / Bifford