I put most of my essential industries just on the surface initially. Once I did start a massive obsidian-cube-casting megaproject, in that game I picked a small hill made of soil as my initial home. Hollowed out the central part, removed ramps on inside and outside. This gave me a walled off area a bit over 10*10 tiles IIRC, plus "walls" 4-10 thick that I could dig some initial rooms in. From there the plan was to keep on living in that Hillfort, or as I liked to call it, mudfort, for the first years, until the first part of the megaproject would be hollowed out and I could make some temporary setup there (using the finalized room layout, but would then rearrange workshops etc. one more time for the actual, final version).
Or you could initially build a work camp on the surface, with dorms and basic industries. Use wood and/or stone (blocks). Build another floor upwards for storage/room, or just use the workshops themselves for storing the end products. Works for most workshops for a while, if you don't order large amount of furniture or something.
The benefit from either of the above is that once you remove all the constructions or channel away the hill-fort, and the grass, shrubs and trees regrow, that part of your embark will look just like any other part that you haven't touched. Well, you might be missing a hill, but noone else will know that.
Or, like others have said, you could designate the more interesting layout right off the bat, and just have storage, workshops etc. out in the hallways for a while. Workshops are also pretty easy to move around, and you don't *have* to have stockpiles for everything before you actually streamline production chains and such.