One of the things that eases you into all the naval terminology (and hoo boy is there a lot) is that one of the main characters, Maturin, is completely new to the sea, so a lot of things are explained to him (and thereby to you). There's a fair bit of that in the first couple novels, then it eases off. There are definitely guides to the books that might help, with extensive glossaries, etc.
The other thing about the series is that once you're over "the hump" the books just sail right by! The first novel, Master and Commander*, introduces the characters, the setting, some of the action, etc. The second novel, Post Captain, is a bit of a slog IMHO but once you get to the third novel, H.M.S. Surprise, the whole series really takes off. There's totally a nautical simile I could come up with, but will spare you.
* "Master and Commander: The Far Side of the World" is the name of the 2003 Peter Weir film starring Russell Crowe and Paul Bettany. It absolutely does not follow the plot of the first novel or any of the others, but cobbles together bits of plot from various novels. Crowe is pretty decent as Aubrey but Bettany as Maturin is considered a poor choice by most fans. Give the film a gander when you've completed the series.