I would count from your primary job until you reach the shipping facility.
You can count miles from a business location to another business location. So the trip from your primary job to the first pickup qualifies, but not the trip from the shipping facility to home.
As a side note, for tax purposes you don't get a mileage "reimbursement"; it is a mileage "deduction". In other words, you don't receive the actual cost of mileage back in refunds, but rather you don't pay taxes on that amount.
Also, be aware that being an Independent Contractor involves you paying self employment tax in addition to income taxes. Depending on your other income and circumstances, self employment tax is usually about 15.3% of your profit (after your business expenses, such as mileage), in addition to income taxes (Federal is often 15%-25%, plus State taxes).
You may want to fill out a new W-4 at your primary job to have more taxes taken out.
