You have 2 choices, 1. is to draw a frame and attachment points to keep your parts together, (what most modelers are use to seeing) 2. is to use the tape, (ala Foto-Cut) The tape also acts as the resist preventing the etching from the back side. If you use the frame method, simply use the marker on the back side, it will stop the etching there. If you are really good, you can try a reverse drawing of the item on the back, and etch from both sides. Cuts down on the time. (this is what commercial etchers do.)
Cutting away as much excess brass, cuts down on the time needed also.
To do relief etchings you need to do it in stages. draw your item, start etching, when it reaches the point or thickness you want, remove the item, wash it in a solution of water and baking soda, to neutralize the acid,. and rinse and dry. Then you need to draw on the area you do not want etched anymore, then put back in the acid.
The sharpie method is OK, but if you really want to do much better, and top quality etchings, invest in the proper equipment. One is a good drawing program. Most of us have one already. Do your drawings much larger than the size needed, then reduce to the size needed. You end up with much sharper lines and parts. Some other stuff you'll need will be clear film to print your drawings on, (Really cheap enough) learning to print negatives, applying the proper photo resist (Comes in 2 forms- powder you mix yourself, or already mixed, and probably now days comes in a spray can and not really expensive), exposing it to light, developing it, washing off the unexposed photo resist, then etching it.
Since most home etchings are done one at a time, and really do not use an agitating bath, the etchings usually end up with ragged edges, and do not etch straight downward, or through, but more at a slight angle.
There was a small home etching kit available a few years ago, although I haven't seen it advertised lately, but a friend had one, and turned out his own photo etched parts as good as if not better than Eduard's. Came with an agitating tank and all, and only cost him about 200 bucks.
OH, the sanding we do, on photo-etched parts before gluing really isn't to rough up the surface...... although that happens also, it is to remove the photo resist on the back side of the sheet when made. Another thing is to never pour the used acid back into the original container, you'll ruin the remaining acid. You need to make a solution of baking soda and water, and mix it with the used acid to neutralize it before disposal. I'd also suggest rubber/plastic gloves, and safety glasses, and ALL GLASS or PLASTIC equipment.