Yup, you must _both_ put the perms in your manifest, and then _also_ request them at runtime now (at least for many "sensitive" ones... not sure if there are exceptions for any others.)
Google's docs are very clear that apps are meant to explain the need for perms, and the impact of denying them at runtime... I'd love to see the play store to also provide publishers a way to specify what the impact/loss of features is if you deny them at runtime. Trustworthy publishers would love this, and the non-trustworthy ones... ¯\_(ツ)_/¯