Either you decide to reuse the login password & have the keychain unlock on login or you use separate keychain passwords & put up with the dialogs that are required to unlock it every time a service needs data from the keychain. That is how the keychain is designed.
You can look at third party password manager applications (Dashlane, 1Password, keypassx, last pass…) for alternatives but either the access to the password vault is unlocked or it it inaccessible to the services that need it.
I'd suggest you consider altering the keychain timeout & set the screensaver to lock if you want to have the keychain unlocked but secured if you leave the Mac unattended. You will still get nagged but security is a balance between convenience and practicality.
Check Keychain apps preferences & the settings per keychain (right click or ctrl+click to access them).
P.S. You can have multiple keychains and only the default one can be set to unlock on login, move the passwords to that keychain to remove many of the nagging dialogs.