Low down payment programs on an owner-occupied home do exist, and the exact minimum depends on the loan program and your credit, so confirm the number in writing with a lender before you plan around it. That's the piece that makes the live-in flip cheaper to enter than a standard flip, where lenders treat the property as an investment and want much more down.
The down payment and the renovation really are two separate pots. Most people doing this fund the work three ways. Cash saved before closing, income earned month by month while the work goes slowly, or a renovation loan that lets you borrow the purchase price plus an improvement budget in one mortgage. The renovation-loan route requires plans and inspections and moves slower, so ask a lender what it involves in your area.
A rough picture on a $200,000 house. Say 5 percent down is $10,000, closing costs land somewhere near $6,000, and you want $15,000 of cash for the first phase of work. That's around $31,000 before you own a hammer. Change the price and the numbers move, but the shape holds.
Ongoing costs are small. A spreadsheet does the accounting most people need. Tax software that handles a home sale runs under a hundred dollars, and a tax preparer who understands the residence exclusion will charge a few hundred more. What you should budget for instead is a permit line and an inspection line. Owner-occupants routinely forget those, and permit fees vary a lot by city and county.