Unfortunately, the filing of an application for an online publication is not a simple process. It involves some unsettled areas of copyright law -- most notably group copyright registrations and online publications. Partially, that's because there has been some uncertainty expressed in recent cases as to what group registrations actually protect -- the collection or the individual units of content. Then, there's the fact that the Copyright Office still hasn't taken a position as to whether an online work is published or unpublished (a fact that also affects your registration).
So what's the answer?
First, you need to sort out who produced the content -- you, employees, or freelancers? If you or your employees created the works, then you are the copyright owner. If you own copyright in all content, you can register that content by following the guidelines in Circular 66. You should register the journal on a periodic basis -- perhaps timed to major article releases. (There's a saying among patent lawyers: register early and register often and that would apply to your quarterly magazine.)
If you're revising the online work, and the revisions are published on separate days, the only for-sure guaranteed protection for the content is that each version of the online work must be registered individually, with a separate application and filing fee (unless it qualifies under one of the two registration exceptions set forth in Copyright Circular 66). That can get expensive at $35 per application but in today's litigious over-legislated world, that's the only surefire guarantee of claiming statutory rights. Make sure to list the titles of all articles in the journal. If you don't claim copyright in individual articles, you may wish to claim the collection of articles -- not necessarily the content -- and you should consider serial registration as explained in Circular 62B. If freelancers created the articles, you don't own copyright in the individual articles unless there is an agreement in place. (If a freelancer owns copyright the freelancer should register his or her article using either the eCo system or Form CO.) Whew!
Just in case you weren't aware ...
Copyright registration is not essential for claiming copyright. You get that automatically. But if you want to claim statutory damages or you want a shot at attorney fees, registering the work prior to infringement is essential.