For developing a budget, I went to www.vertex42.com and downloaded a few of the budgeting spreadsheet tools, found one that worked for me, modified it a bit for our needs, and used that. We also opened 2 more checking accounts and an online emergency savings account. When we recently met with our financial adviser he mentioned the "bucket" budget, so this is like that, only with bank accounts.
One account is for regular bills (mortgage, utilities, insurance, etc.) that will be paid online. I take the monthly average from the budget spreadsheet and deposit into that account. Since some of the payments are not paid monthly I use it like an escrow account and know that the money will be there when the bill comes (this was a problem in the past). That also removes that amount from our regular checking account where we "swipe the card". We don't have a debit card for that account since those bills get paid online.
The other account that we opened is for household expenses (groceries, household items, dining) and our monthly budget gets deposited into that account. We each have a debit card for that account but stick to the budget. We found that these items created the most "leakage" in the past.
I've used Quicken for several years and paid bills through it. Now I pay bills through the bank's website and just use Quicken to track expenses. I also use Mint and will likely ditch Quicken at some point.