You can do the bottom both ways you asked about.
I like to epoxy saturate the wood and let it cure before glassing , Here is why.
The epoxy saturates the wood (soaks into it ) which helps to strengthen the wood plus it puts that coat of epoxy there to help protect it from water damage in case something penetrates the layer of fiberglass. It also gives the epoxy you will use with the fiberglass something to chemically bond to. You do have to wait for 24 hours before doing the glass work.
If you decide to do it that way it will require a little extra work.
The epoxy soaks into the wood and the outer fibers will rise up as the epoxy cures , this causes what I like to call , whiskers. The whiskers need to be shaven before the glass is applied and you do that with a light sanding , really light sanding. You need to remove the whiskers because if you don't and you lay the glass on the boat the whiskers will grab it and cause runs ( gaps ) in it.
If you run your hand over the wood you will be able to tell if all the whiskers are gone , a towel can be substituted for your hand.
Then lay down the glass and epoxy it to the bottom.
The epoxy saturation and then the fiberglass with the epoxy might strengthen the bottom so a runner would not be needed. If one is needed then consider it a sacrificial item since it will wear down over time and need to be replaced.
Chuck.