There are three on-going series right now. One is "Transformers: More than Meets the Eye", second is "Transformers: Robots in Disguise", and third is "Transformers: Regeneration-One". There is also the Transformers Prime series, but personally as an avid Transformers Comic Book Collector, I don't consider it as one of IDW's main story line.
Anyway, More than Meets the Eye and Robots in Disguise are linked with each other, so I highly, HIGHLY suggest that if you read one, to be sure to read the other, because they take place in the same time-line; However, Robots in Disguise
follows Bumblebee, Prowl, Arcee, and a bunch of others on Cybertron, trying to rebuild it. More than Meets the Eye
follows Rodimus, Ultra Magnus, Cyclonus, and more, on an exploration trip on a quest to find the Knights of Cybertron. Out of the two series, I'm having a lot more fun reading Robots in Disguise right now, but that doesn't mean More than Meets the Eye is bad, because it's not. It's just currently at a down/slow part of the story, where-as Robots in Disguise is still a lot of action and espionage.
Now, with Regeneration-One, it resumes after the original Transformers comics (The one by Marvel in the 80's). I believe it's 20 - 25 years after the last Marvel Transformers comic, so the FIRST IDW issue of that comic is technically issue #80.5, which is the Free Comic Book Day comic. Then the first "true" issue is #81. This is a limited series, because they plan on only doing it up to issue #100. That's the issue they plan on ending Regeneration-One.
I know a FEW people are not satisfied with Regeneration-One, because they feel that they changed and screwed up the original Marvel story; However, personally, for me as a Comic Book collector and enthusiast, as well as being a Transformers fanboy, I'm satisfied with it so far and most other readers are, as well.
I hope this helped you.
On a side-note, I forgot you asked for a website where to purchase these comics. Personally, I go through Midtown Comics for all my current comic book needs (I also collect almost ANYTHING Gotham City related, I.E. Batman, Birds of Prey, Catwoman, etc.).
Midtown Comics: http://www.midtowncomics.com