If you did not incorporate the business - it is considered your solo proprietorship and generally - you should attach schedule C to your personal tax return to report business income and expenses.
Start-up cost - expenses you had before the business started - in general should be amortized over 15 years.
You can write off up to $5,000 in startup costs and another $5,000 in organizational expenses in the year that you start your business - thus in the first year you will deduct 1/15 part of the total expenses - and so on in following years.
If you haven't started the business yet - you may not deduct any start-up cost.
please see more details in the IRS publication 334 - http://www.irs.gov/pub/irs-pdf/p334.pdf
Please let me know if you need any help.
If you tears both locations as ONE business - you do not need to account separately for each store.
In this case start-up costs should be combined and accounted only before the business started.
If you have any additional cost AFTER the business started - that is expansion cost - and not a start-up cost.
As start-up cost is amortized - so on the schedule C - http://www.irs.gov/pub/irs-pdf/f1040sc.pdf - it is reported on the line 13
To determine the actual amortization amount - use the form 4562 - http://www.irs.gov/pub/irs-pdf/f4562.pdf
Expansion cost of the existing business is deducted as any other business expenses.