This presents some problems - if you want to keep the grounds separated, (lets say to control noise induced by ground currents) then you can make your own part versions with non-power-port pins (flag "Power Symbol" must be cleared (In libedit, Part Properties/Options).
Some parts call ground pins GND while others may have it as VSS - you can connect them with power symbols for these names. There is some other foot work needed with the use of a PWR_FLAG to prevent ERC from detecting them as unpowered.
Best Practice It is popular to not bring out the power pins on parts - and let power be automatic, this practice might save time, but at the cost of failing to communicate what is going on. A better way.
Create separate power units for logic chips and opamps and put them and their associated bypass caps below the main circuit. This helps to show which bypass-cap is intended for which chip. It also suggests that the bypass needs to be close to the chip it is bypassing.
Don't use invisible power pins. Current flowing on ground returns create voltages - seeing the power connections helps prevent noise problems.