Yes, there's a big difference. You should enter the expenses related to earning the 1099 income, in the self-employed business section and enter the expenses related to the W-2 under the Job expenses section.
Expenses deducted as self-employed are far more advantageous. Musical instruments would be assets if you use them to earn income and they last longer than 1 year. If they're less then $2,500, you can select the De Minimus election to enter these costs as expenses, which the software will ask you about under self-employed Assets/Depreciation. You'll need to determine where to deduct your assets based on the above information. If you are primarily self-employed it may be easier to enter them only in that section and enter a percentage for the amount of time they're used for earning self-employed income.
Self-employed expenses are deducted from your related income on a schedule C, before the net income amount flows to your personal tax form 1040. Employee job expenses are an itemized deduction, so your total itemized deductions must be greater than the standard deduction ($6,300 single/$12,600 married) to get any benefit. Additionally, your total employee job expenses are first reduced by 2% of approximately your total income (AGI - a subtotal on your form 1040 line 37).
