if fence/blade are aligned marks should be reduced, try a caliper (vernier) to check if the blade and the fence are parallel. Use a splitter. Id even check that the blade isnt "wobbling" (right english term?), with the cord unplugged place a marker on one side of the blade edge before the teeth just that barely touches and leaves a mark then turn the blade slowly, if the marked line isnt consistent and/or disappears you know the blade doesnt run true, to me checking that beyond the marker method for extreme small movements its a little overkill. Eventually light marks come off and if you use a small plane on the hull, in and out, they go away so fast that theres no need to worry too much about them.
For the rest id use a splitter along the outfeed table, something like this http://www.leevalley.com/wood/page.aspx?c=1&p=51151&cat=1,41080,41165 its easy enough that you can build 3 or 4 by yourself, or set a strip (metal or plastic) in a slit in the outfeed table, if you use a straightedge against the side of the blade you can set a long-ish splitter from the back of the blade out and use that as fence, you cant really press against that so i wouldnt use a really pushy featherboard on it but it should be enough for you to guide the board straight all the way, use the straightedge to set the half fence before the blade so that splitter/fence are parallel.