From what you have said it appears to simply be a matter of mortaring pavers in place and putting a bit of mesh over the drain/grate to keep it clear when it it covered over with pebbles. Roadbase is mainly for leveling and providing a secure base...you already have a secure concrete base and can level using the mortar.
The gaps between the pavers where the river pebbles are going will be sufficient to allow drainage to operate as it does at present assuming the pavers are not being placed totally across the width of the path. If so embed plastic piping in the mortar to run under the pavers and allow flow to drain.