I've had my Paypal linked to my main checking for years and never had a problem. I opened a second Paypal account that was non-business (not accepting credit cards) for SR cashouts and needed to use a second account for that. The ONLY reason I have two checking accounts at my bank is because the temp agency I was working for last year screwed up payroll one week and deposited, then TOOK money out of my account. I opened teh second one to protect myself from them because I didn't trust them after that.

If it gives you peace of mind and is free, go ahead and open the second account. Just leave a minimal balance in there (mine still has $1.00 and I haven't used it since going permanent in January.)