REgarding what plants to use, it depends on your conditions - sun, shade, etc - I think it's been discussed here before, or in the landscape design forum... search for groundcover + flagstone perhaps. Re what to do first: flagstone first, plant last.

Any ideas? I'm going to call local contractors soon, but I'd like an idea on what to expect and recommendations for replacing the rock with a stable surface. I'm thinking of adding pavers to the perimeter because it will probably be easier to get someone to to do a small job of pavers than to get a small concrete job done. Plus, I assume pavers will need less/zero long term maintenance and upkeep, but can pavers be done around the jagged outlines of the existing flagstone?

Thanks for all your comments. From our existing patio/side yard, we cannot clearly see the backyard. We thought it would be nice to create a sitting area with a good view of the garden. We considered the patio along the back wall of the house, but felt in that case, folks in the current patio and new patio cannot see each other. Another incentive was these trees provide a lot of shade so we thought it would be fun to sit beneath it. https://www.dropbox.com/s/10n839mhi0fwz5r/backyard-design.jpg?dl=0 Here is a rough sketch of the backyard where the trees and planter boxes are already there. We are just planning to add a small section of lawn, add decomposed granite around the raised bed, separate the trees with a bender board and add mulch to it, add some border flowering plats and add a place to sit and relax. After hearing all your inputs we are not too keen on putting the patio around the tree now. May be adjacent to the tree or near the back wall of the house ? Any comments/suggestion on the above design is welcome.

Thanks Floral, though faint (the plant is tiny) rank is a good description of the scent. I moved it before seeing your response and the link. I’m on the lookout for native plants that are somewhat aggressive whether perennials or enthusiastic reseeders. I have a lot of areas - basically the transitional areas between the lawn and the woods. As for conditions, there‘s a little of everything. Some areas are full sun, part shade or dappled shade; clay, and rich loam soil; dry and moist. A constant among them is that our yard is a deer haven. They eat everything except barberry, poison ivy, garlic mustard and any number of other nuisance plants. I’ve come to accept that deer resistant means, generally, that the plant can tolerate being browsed (or even benefit from it, like a forsythia hedge). This might not be the right forum to ask, but suggestions are welcome. Thanks!