@asb3pe
For 2x2 trees you need to give the cart a "Planter Range Extender" (I think that's the name) lets you tell the cart to plant saplings up to 7 blocks - I think it's 7 - away from the tracks. (only put it to 2 away though, the higher numbers are meant for trees that need more than 2x2)
To change a cart after already making it you need the "Cart Modifier" upgrade for the assembler-block. With that you can put the cart into the assembler and change stuff around (of course that costs time and fuel again). Great also when you want to make a new cart, like with a better wood cutter, and not want to craft every part new.
And you will need an "Advanced Smelter" in your cart. With that you can tell it how much you want to smelt into charcoal and where it should put it.
I usually had 2 advanced smelter in my treefarm-cart one to refill the coal-generator with charcoal and another to make extra charcoal into the inventory. Though I don't know if that works with GT, not that far yet (I play too many pack *grumbles* ^^")
Oh and just in case: You need to tell it 'what' you want to smelt. Just place a wood in the first slot of the smelter so it know what item to look for in the inventory to smelt it.
[edit]
Oh yeah, with the planter range extender you might want to try around if you actually want it. Problem is that it has a weird planting-way for these tree. Especially when it comes to corners.
Try not to make too many corners in the track or it can mess up alot (so it doesn't plant the best possible way).