If they're soft roots... Ive been digging them out. Then again, I know mine originated from a crappy ol' tree and its in the middle of where I am planting my lettuce this year. Depending on the depth of the root, you may be able to plant around them. (i did it last year with very little issue, as I was too busy to take them out) Hope this helps at least some what.

Thanks for your response...I think i will just work around them for now.The roots I'm coming to are hard and almost 2in in diameter. I am going to need to spend more time getting that area ready so I planted my marigolds in 3 very large containers in the yard :) had just enough soil and pots :) now I need to actually take my time and plan a little better!

If you have any dry leaves, place them at the bottom with your soil on top and they will eventually decompose--but in the meantime, they will help to prevent weeds growing through.

Don't make the layer over the tree roots too heavy, though, or it may smother the tree roots.

Lookup "lasagnia gardening" for more on this.

Your plan to spend more time getting the area ready sounds very reasonable. Even if you don't add a bunch of 'dirt' or amendments, by making sure the weeds you pulled are dead (and not going to grow back from the roots as some plants can,) you can expect a much easier time after you do start to put desirable plants there. Weeding never ends, the wind blows seeds, and birds and squirrels move them around constantly, but once you get things under control, it should be very easy to notice wayward sprouts in such a small spot and pull them while they are still infants and come up easily.

Since there are tree roots there, I might not add anything but some mulch. That helps moderate moisture levels, in both times of drought and pouring rains. It also makes it harder for many unwanted sprouts to even get going, and easier to pull if they do. An organic mulch that decomposes over time will also add a measure of fertility to the soil, as well as improving the texture. Leaves make a fine mulch, though the cost of a couple bags of store-bought shredded wood (not painted, or with anything added,) would be reasonable for that small area and always looks fantastic, 'finished.' You could sit the pots there on top of the mulch while you're waiting to see if any of those roots keep growing unwanted plants.

When planting around tree roots, I don't try to cut through the big ones you described, though doing that to a few in such a small area won't hurt the tree (or shrub) if you need to cut some to be able to use the space. Cutting them a double-edged sword, since it will usually cause many more roots to grow from the end that's still connected to the tree or shrub. When planting perennials (plants that come back after winter,) it's not as much of an issue as it is in a spot where you want to be able to dig holes for annuals (plants killed over winter) annually.

A happy medium where annuals are preferred might be planting some seeds, which can find their own way around the tree roots. The seeds sold at seed racks are mostly fast-growing annuals that reliably have time to make flowers well before danger of frost (assuming they are sown when/as directed,) hence their enduring popularity. Marigolds are in this category.