Use rclone config for interactively adding remotes. Those remotes can be mounted (in a FUSE layer) or accessed with commands like copy.
The remotes can be layered, so you can create a remote of the crypt kind and point it to another remote, so you can encrypt your files in the remote.
The command rclone test info can tell you which kind of file naming the remote supports (do it in the root remote and not on the crypt layer), so you can use larger filenames when configuring the crypt remote (e.g. base32768).