Salaried and Freelance Work IT Planning

Yeah you are eligible for claiming the presumptive taxation benefits as per sec 44ADA as you are coming under the definition of professionals under sec 44AA ,who are eligible for 44ADA.
But the total professional receipts from all the projects should not exceed 50 lakhs per annum , otherwise you are not eligible for 44ADA .
so make sure that distribution is made to get the benefits of being eligible for 44ADA .your wife is also a specifies professional eligible for claiming under 44ADA .
You need to apply for registration under GST ,if the threshold limit of turnover is exceeding ,please refer sec 22,24,25 of gst act for applicability of registration under GST.