Here's my process when I brew one gallon batches, (actually closer to 1.25 gallons). Like you I'm also fermenting in the 1.4 gallon Little Big Mouth Bubblers. I bought a smaller siphon from my LHB shop and I siphon into a 2 1/2 gallon food-safe bucket I picked up at Lowes. I drilled a hole in it and installed a spigot. I have a two or three inch long hose coming off the spigot and a bottling wand attached to the other end of the small piece of hose. I rack to the bucket (no sugar at this point). Using a tip I picked up from
@TwistedGray I use a sanitized funnel and measuring spoon to add between 1/4 and 1/2 tsp of table sugar (depending on style), to each empty bottle. I rack the beer on top of the sugar, usually getting 10 to 12 bottles per batch, and then cap the bottles.
I haven't really had an bubbling issues with the siphon as long as I keep it fully submerged. Have you tried a different siphon?