I understand the inconvenience of dealing with a 529 that is owned by someone else.
Two things to consider:
1. There is now the ability to roll over up to $35K of excess 529 funds into the beneficiary's Roth IRA. It's a pretty nice deal. One of the requirements, though, is that the 529 account be in existence for 15 years as of the date of the rollover. If this is of value to you, you might look to see when the various 529s were opened to see when the 529->Roth rollover option would become available. If your parents started theirs before you started yours, it might be worth dealing with the inconvenience.
2. If your Dad is amenable, you could discuss rolling the 529 money from his 529s into your 529s. Generally this is a tax free event (doublecheck with your Dad's 529 plans to be 100% sure). It also reduces the number of accounts and generally simplifies things, and would help you avoid the inconvenience factor. However, if his 529s were older than yours, it may delay or impact your ability to do the 529->Roth rollovers noted above.
And I agree with the other poster. What I typically did was get the bill from the university, distribute that exact amount from my kid's 529 into my checking account, wait for that transfer deposit, then pay the university directly. Worked fine.
In one case involving my Dad's 529 for my niece, I did do a direct transfer to the university for her bill (as my Dad's POA). It was a bit convoluted because I had to get the correct mailing address and university account number for her, put that into the 529 website, and then I was in the dark until the payment arrived and got applied. But it all went just fine in the end.
