Yes the self employment tax is in addition to any regular income tax on the Net Profit. It's for the FICA (SS & Medicare) tax that isn't taken out like on W2 wages. You pay 15.3% SE tax on 92.35% of your Net Profit (If it is greater than $400). The 15.3% self employed SE Tax is to pay both the employer part and employee part of Social Security and Medicare. So you get social security credit for it when you retire.
#3...yes a Single Member LLC is a disregarded entity and is filed on Schedule C same as a sole proprietor or self employment. You pay the SE tax on all of them.
