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Castlevania RPG is broken up into games instead of books or sections or whatever you want to call them. Each game is in multiple chapters, for ease of consumption. There are also numerous backstories, side stories, and random stories to choose from.
As a suggestion, and this is only suggestion, from here you should move onto the main story (that which is covered in the "Archive by Chapter" section of the menu) and read the first game at least.
Once you hit "Castlevania RPG Year One" (technically a prequel) you can either choose to continue reading from there, or come back to it and go into the bonus archives.
If you delve into the Bonus Archives, read the backstories: "Out of the Darkness" (Darkmoon's tale), "Journey of the Holy" (Alec's tale), "Spell Failure" (Katrina's tale), "Bunny Tales" (further tales of Darkmoon and his familiar), and "Tales of the Fallen" (Angel's tales).
After reading those, you may want to go back to the main archive, and continue reading from "Year One". Read from here, through to "Castlevania RPG Gaiden", and then stop again.
Your next stop should be back in the Bonus Archives to read the "Castlevania RPG Meets the TMNT". While you're at it, get caught up on the random bonus comics, such as the "Supplementals", "Mini-Arcs", "The Random Adventures of Frankie and Mummy", and "Frankie and Mummy: Monstrous Detectives".
After that, you're good to go back, pick up with "Castlevania RPG Gaiden", and read right on through to the present strips.
But, again, that's just my suggestion. Really, you should be able to read them in any order you so choose. Some off-hand jokes may work better if you read some things in a particular order, but it's not essential to the story.
Oh, and when you're done, go check out "DSWC". It's my other comic, and it ties into CVRPG.

When evil spreads across the land, and darkness rises and the monsters roam. When the creatures of the night make beautiful music, and the things that go bump in the night go bump with greater enthusiasm. When the world is in peril and is in need of a hero...

These guys are, sadly, the best the world can hope for. These are the adventures of the heroes of CVRPG. They mean well, they try hard, and occasionally they do the impossible...

They actually do something heroic.