I have always put a strip of glass tape and epoxy on both the inside and outside of the seams when putting the two pieces of long panels together (I use butt joints because I'm not that good with making a scarf and I want to make sure the seam will hold through stitching).  I just sand/scrape the edges of the tape smooth and level.  The seam pretty much dissapears when I put the sheet of fiberglass over the outside of the hull.  There is probably a slight hump if you look really closely, but by the time you get all the fill coats on the hull and sand everything I don't think you notice it.

If you have any bubles in the taped seam you'll want to get rid of those of course. 

I did the same thing. I did not sand it clear, nor did I sand it as smooth as I should have. As I am nearing complete I am seeing that I should have sanded it complete or much better than I did. This is my first build and that mistake was made very early in the build process (months ago) and as I am nearing complete I will now use paint for the bottom and sides, at least in some areas. If you are going for varnish and seeing what I have done I would sand it complete.

Are  you working with a butt joint or a puzzle joint? I have no experience with butt joints, but i built two Shearwters with puzzle joints. If you are concerned with the appearance, sand right down to the wood, and tape the other side. If you leave a hump, it will increase the number of fill coats needed to level it. The 9 oz. tape is pretty chunky stuff. If you thickened the epoxy with silica, it may look cloudy not matter how much you sand and fill it.

On my second build, I actually skipped the tape on the two puzzle joints of the bottom panels. Puzze joints more than double the panel-to-panel joint length, and these joints in the cockpit area recieved a layer of fiberglass anyway.

It's puzzle joint. I have sanded it smooth but have not sanded the strip of glass till it is gone. Does the strip of glass have to be sanded till it is completely unseen by eye, so that nothing will be seen when I glass the hull?

Caution.  Don't go to far.  If you fair the edges of the glass, you can be pretty sure it will disappear when you glass the entire bottom.  If you sand to much you will go thru the outer layer of veneer and there is no way I know to hide that under varnish.  This is the bottom of the boat and generally, no one will ever see it.  My Shearwater is over two years old and I have not had it upside down to look at the bottom even once.  Add launching scratches that will start to accumulate immediately and there is just no reason to worry about this.  Relax and enjoy your build.

If in the end you do not like how the bottom looks, coat it with 50/50 graphite powder and epoxy.  It will hide everything and give you a bullet-proof bottom.

PAG