Welcome to the world of security clearance processing! To answer your statement at the end of your post, yes, you are at the very beginning of the process.
When I was first accepting a contractor position (Secret as well), the company sent a set of initial security questions. This essentially verified citizenship status and basic information about me. My guess is that is what you’ve just been asked for.
Following these questions, I was sent a security prescreening, which was essentially an abbreviated SF86 form, asking most of the questions the SF86 asks. I believe that this form is used by the FSO and the company to know of any sort of major problems that would be included on the SF86. Long story short, a company isn’t going to want to pay for someone to go through the clearance process if they believe they won’t be granted clearance. I wouldn’t be surprised if you’re sent something similar shortly.
Then comes the SF86… the thing is quite literally a beast. It sounds like your company uses the eQip which will make things much easier than the paper version, but it will take time. Be sure to be very accurate and thorough in filling this out. Put in the extra time to make sure that all of the little details are spot on, as well as verifying that all reference contact information is accurate and up to date. This will make things much easier, and likely, much quicker to review. I would also be expected to submit your fingerprint cards (likely via mail if you aren’t local, otherwise, they may do it with you) around this time as well.
After that, you play the waiting game. I’ve seen interim decisions come in as little as 2 weeks. I’ve seen others take a few months. How easy these are to get depends on who you ask. Rumor has it interim Secret isn’t as easy to get as it used to be, but again, I’ve seen it go both ways.
Really only you know what kinds of hurdles you may face for the clearance. Take a look at the 13 adjudicative criteria and you should be able to gauge for yourself roughly how troublesome your case is. Depending on those issues, you may or may not be asked for an interview, in which you can try to further mitigate negative information (more so than the comment sections on the SF86 allow for).
Full clearance timelines are in the same boat as interim in that they can be all over the board and really depend on your case. I’ve seen some go through in a few months, and also seen horror stories of well over a year.
Best thing you can do is be thorough and forthcoming on all of your security forms and on the SF86. Anything besides that is completely out of your hands.
Best of luck!