Hi,
1. You must regiter autónomo, or the accountant of the company can do it for you, your fiscal number will be your NIE and the company will see you are registered when they have to pay your IRPF. You cannot say you will regiter and not do it. A lot of companies also ask for the 036 or 037 (i think) registration models. I don´t have only one company that I invoice, I work with several and I cannot "lie" with regards to my registration. One, because I put IRPF and IVA and two because they pay the IRPF for me in Hacienda and as I said they deduct my bill as an expense.
2. That is what you have to understand. The IRPF is paid directly by the company to Hacienda, 15% of the 1000, not by you. You have to pay, every 3 months the VAT. If you balance the VAT you invoiced with VAT from your expenses, you don´t pay anything, but if you don´t you will have to give the VAT to the Hacienda. I was not careful, did not have a lot of expenses with VAT and had to pay for the last 3 months 740 euros and believe me- it hurt.
Check with the company the exact situation, because they will have to pay the IRPF directly to the Hacienda for you-150 euros, you will have to pay the VAT, every 3 months if you cannot balance it, plus income tax if you don´t put any invoices as expenses (rent, utilities, phones, gasolina,etc.).
Registering autonomo is not easy and you have to see if it is worth it and also see what an accountant will charge you. I pay mine monthly, but there are some that charge only every 3 months, when the tax has to be done.
Good luck and I hope I answered your question.
Valentina