I'm a tad bit rusty but unless there have been significant changes in the past couple of year....
(Keep in mind Your state may have laws that are more generous) but in general, under Federal law you have the 12 weeks per year. Your employer in their plan can designate if it's a rolling 12 months or per calendar or fiscal year. Usually it's a rolling 12 month period.
Your employer can choose to require you to use up any paid leaves you have available and count those same days in the 12 weeks.
Basically, you may have sick time, or short-term disability as paid leave, and whether or not you use or are required to use up your sick time, those days count towards your FMLA 12 weeks.
Any absense in excess of 3 days can be FMLA but there is notification required, your employer needs to formally notify you that you or using FMLA leave days for the 12 week clock to start.
Also, intermittent leave (as in a reduced schedule) also counts against the 12 weeks of FMLA leave. So if you had to work half time per Dr. orders for 10 weeks, that would use up 5 weeks of FMLA protection.
FMLA is not paid leave but paid leave can count against the FMLA leave. Basically as someone already said, FLMA offers you some protection but not a guarentee of the same job when you return, rather a like/similar job and pay.
Employer's can always give you longer leaves, paid or unpaid, but they are under no Federal/legal obligation to do so.
If you have been notified that you are using FMLA time, any hours you take off (paid or unpaid) will be counted against the 12 weeks. If you are not notified of your FMLA rights the clock hasn't legally started yet (a loophole some employers overlook)
BUT - this info is from back a couple of years when I was a qualified neutral/mediator. I am not an attorney and have not kept current on any changes in the past couple of years.
AND - I know some public sector employers are exempt from Federal laws such as FMLA. If you work for the government they don't always have to follow the same rules
Check out
http://www.dol.gov/esa/whd/fmla/
and check your State department of Labor for any local rules