They might add up over time - but it would take a LOT of blocks to get ton ONE bitcoin on transaction fees alone at this point.
To get back to the OP, the cost of mining has ZERO significant effect on transaction fees right now, but that will eventually change as the block rewards keeps getting halved - most likely won't be significant for a decade or more though.
What is the best way to mine? Any advice?
Move to an area with VERY VERY cheap electric, then wait for the 14/16nm Full Custom machines to start getting produced - or look seriously into various Altcoins for the short term. Possibly both.