@Jonnybegood 

"I then charge the freight to my customer. When I do a project P&L it shows up as income: why. I paid the freight to the company how do I expense it. It is a small amount (less that $300 per year). I don't really care to track it but I do want to account for it."

It's revenue (gross income) because you charged your customer for it - no different than any other type of revenue.  The freight charge from the tile store is a materials expense just like the floor heat cable and t-stats.  If you pass through the freight expense to your customer (no markup), then the materials expense offsets the revenue and you have no net (taxable) income.    

"Also I am considering adding a one-time trip charge to my estimates to cover cost to pick up materials as my supplier is more than a hundred miles from me and most of my jobs. How to I add it and under what account(s) do I put it?"

That's up to you.  It's revenue to you so set up a 'Trip Charge' item or add it to your total job cost.  Either way works as long as you assign the charge to an income account in QB.