I have taken a position on the same scrip, but on different days. Can I square off the second order first under 5-Day Margin trading?

No. FIFO (First In First Out) method is followed for square off. Example: Assume you have bought 100 shares of ABC on Monday, and 40 shares of ABC on Tuesday. If you want to square off 110 shares, 100 shares bought on Monday will be squared off first, after which 10 shares from the shares bought on Tuesday will be squared off.