I'd think twice before giving superuser (sudo) privileges to a third-party application i.e. entering your admistrator password when it asks you to...
Open Terminal /Applications/Utilities/Terminal.app
and type the following:
sudo periodic daily
sudo periodic weekly
sudo periodic monthly
If you want to type less you can also just run them all together i.e. like so: sudo periodic daily weekly monthly
You will be asked for your administrators password, but in this case you won't be giving it to an application that is in essence just a bunch of applescripts in a nice packaging.
You could also just get the jobs to run at a time at which your computer is more likely to be running (defaults are 3.15am for the daily, Mondays 4.15am for the weekly and first day of the month 5.15am for the monthly) by changing the defaults in the preference lists:
com.apple.daily.plist
com.apple.weekly.plist
com.apple.monthly.plist
For anything else 'maintenance' related you need there is DiskUtility.
Should you want to make use of the interface-tweaking options in Cocktail, Onyx et al you'll be sure to find simple UNIX commands all over the Internet that achieve the same.