In a large action, if I buy multiple properties, do I have separate closing costs on all of them or can I roll this in one somehow? do I do a normal mortgage on all of them or roll them into a single business loan? if using a single loan do I keep the property I am flipping out of it?

For some things like title costs yes seperate, for others like escrow you might be able to roll it into one.  A small business loan likely offers far worse terms than individual mortgages or a portfolio/ blanket loan.