My system has a few working parts, but it does the job.
I have all my annual expenses in SmartyPig. It withdraws from my Bill Payment account on a monthly basis. Then at the end of the year, the money is good to go. It's not as convenient as a normal account, so I can't just "raid" it for an impulse spend.
I have a Bill Payment account. All my regular expenses go there. Cell phone, internet, water, electric, mortgage, etc. I set up ACH/autopay for all of them. I have equal payment plans for utilities where I can, and then I over estimate each bill a bit so there is extra if needed.
Every week, I transfer money to the bill payment account. This way it's not a massive transfer at once, and it coordinates with my and my wife's pay periods.
We have a primary checking account which gets our direct deposits. That pays for our incidentals, credit cards and other misc stuff. We also transfer weekly out of there for our personal allowances and our savings.
It took a while to get there, but it works and we're good with our bills.
I also use Quicken for day to day transaction maintenance.