For instance, how is the relationship between the private contractor and the federal agency?
I've heard many say the easiest way to get a federal job is to get experience with a private contractor first.
What all is investigated during getting your secret clearance?
Relationship varies by agency & contract/contractor. I remember when I first started out I was on a contract with department of commerce under general dynamics.. My nikka the relationship between GD and the government was beyond shyt. I kid you not at least one contractor was getting let go a week for 2 straight months. It was just a revolving door. If a govie didn't like the way you sneezed, they put a call in upstairs and next thing you know they just told you to leave your badge at the security desk when you leave for the day. Needless to say when the contract went up for rebid, GD didn't win it.
But on the other hand some contractors have a great relationship with a particular agency and keep the contract for years.
I know a couple cats who went from contractor to govie when a spot opened up. It was pretty much a "who you know" type deal. So it is a helpful way to get in if that's your goal.
I believe secret they go back 5 or 7 years of your history and top secret is 10. This is all your past residences, education, workplaces, financial record, civilian record, any place you traveled to, etc. for that time period. Best thing to do is be honest about everything, if you lie about anything they will find out and you will not be getting a clearance.

ever again