Vacuum, wash and dry the interior before you start sanding, if your haunts are anything like mine, there will be some sort of sand grit kicking around, these can cause scratches if they get under the sandpaper.
Use the manufacturers regime for successive coats, I believe Epiphanes is something like 50/25/10 (thinning for coats 1/2/3), I alway thin at least 10-15% even for finish coats ... personal preference.
First, I would go over those patched areas with the same regime of the original varnishing .... I would add a couple of inches around your sanded area, moving each coat towards the overlap sanded area, final coat to feather to the edge of the sanded area. This will put ~ the same protection on the patched area.
If you have any areas of deep scratches or other areas that need extra attention, sand them out before you varnish your patches, use the same idea of feathering the coats to an enlarged sanded area. You can then touch up all the "special" areas at the same time ... saves some effort. Don't worry about making them look pretty and blending, just get a reasonably smooth application.
If the inside is finished with a matte coat, you can sand somewhat more than lightly, simply because matte varnish doesn't have the integrity (strength/UV protection) that gloss does, so removing most of it is not a bad thing. I use 220 grit with a foam block to sand out the interior and "scuff" the finish, make sure to knock down the restored areas enough to just kill any shiny areas.
Vacuum the interior, check for any shiny areas and scuff any you find ..... finish with the vacuum and a tac rag wipe out.
Since you have addressed any serious areas and the protection has been restored to the interior, you only need a top coat to make it all look even and then a matte coat if you want to kill the shine. So I would just use ~15% thinned gloss coat on the interior ( I like the roller and tip method) .... if you aren't doing the gunnels, have a set of blocks ready and flip the hull to dry.
Once this is dry and set (next day usually) if you intend to finish with a matte coat, rescuff and apply your matte finish .... again, flip the hull to dry.
Flipping is optional, but it does serve a few purposes, it allows the vapours/organics to leave the inside easier (otherwise they can tend to collect in the canoe cavity), it also prevents dust and such from settling on the surface ...
Brian