VAT is a 303 model, it shows all commercial income and expenses (both with and without VAT). As a result, if the VAT balance is positive, it will be necessary to pay this VAT by the 20th day of the month following the end of the quarter, and if it is negative, either leave it for offsetting in future periods or request a refund. You can carry over up to 4 years to future periods, then this overpayment (when expenses with VAT are greater than income with VAT) will either burn out, or you can request a refund. Everything is exactly the same as for LLC.
Income tax is model 130, where all income and expenses for the trimester are entered. Social security payments are also included in expenses, in addition, those working from home can include expenses for water, electricity, apartment insurance, communidad, in a proportion corresponding to the share of the workplace in the apartment (indicated in model 036/037 at the beginning of economic activity as an individual entrepreneur).