To get started, you will need to register a school login with Home School, Inc. Then you will register another user for the teacher/parent, and a user for each student. This process is a little irritating and I would recommend using a single password for the school and for the students. Each time your student logs in, they will first log in to the school and then select their name and log in AGAIN to get to their account. Depending on the ages of your student, this can feel like a lot of passwords to remember. Fortunately, most browsers support saving the school username and password which should be relatively safe if you are using the same computer at home. 
Once you, the teacher, are logged in click on the link for the "Planner" and get started. There is some very easy to follow set up dialog for your School Info and School Term. Here my recommendation is to keep the terms SHORT, five to ten weeks at max to allow for changes in interests or schedules. It is very easy to copy the courses from one term to another so keeping the terms short actually alleviates extra work instead of creating it. Once you have a term and at least one student, it is time to set up those courses. You can use the "Make A Plan" interface which will guide you through the process or go straight to "Courses at a Glance" for a faster interface. 
Creating a Course is self-explanatory. You should select a grading method. - for us it is usually complete/incomplete - but, if you use a grade-driven curriculum or have a child that thrives on numbers, do what feels right to you. Even if you choose the complete/incomplete options, you will have an opportunity to grade specific assignments or record comments on a topic. You will also need to choose a time for each course, this really doesn't mean that you have to do it then; however, you should really estimate how long each topic takes in a day so that you can get an accurate picture of the time spent in school (especially if you live in a state with an hourly attendance requirement). Most of our core subjects take about an hour +/-. Once the Courses are created, you will add coursework and assignments to it (again, this is where shorter terms will be easier). There are good Template "tricks" for making incremental lessons or repeating the same task each day. When all your courses are ready to go, it is time for the student(s) to take a crack at it.
The student will again log on to the school account first. From there, they should click the link for the "Planner" and then select their username from the list and enter their password. The student will be taken directly to their "School Today" screen. This terrific screen allows the student to see what their tasks are for the day and "Do Work". Clicking on the "Do Work" tab opens a dialog box for that subject and once they have completed their tasks for that subject, sends the work to the teacher/parent for review. This screen also shows the student any past due work from earlier days and what work is still awaiting teacher review/grading. 
Again as the teacher, you will log in and see work that is needing your review. If you have set the course or assignment as requiring a grade, you will fill this in as you complete your review. You can also make other comments in this dialog box or review your student's feedback. "Bad handwriting", "Only 12 minutes to complete timed worksheet!", "Read from p.394 to 437", "Boring video, Mom" are some of the comments that we have left for each other on our assignments.
Overall review of Homeschool Inc PER is 3.5 out of 5 stars. I like the interface, the dual log in thing is irritating though, especially for younger students. It is FREE which is a plus, but that comes with the big MINUS of ads which are continually scrolling around the right hand side of the screen making the program sluggish at times. The internet based planner can be used from a Mac, PC, or *Nix computer which is a real draw in our family, but I'd also like either an offline syncing interface or export with iCal or some mobile app. There are also many customizable reports, Skip-A-Day, and Field Trips which were simply too much to cover in this post (so I will cover them next time in a couple of weeks).
