Many of the drawing programs may not present the actual details as they occur. I have a method I use for laying out that may help. I take all my wall measurements and details like plumbing, electrical outlets, windows, door casings, appliances, etc. Then I cut out a mock countertop from anything, like 1/4" plywood, or, if it's to be a laminated top, the actual 3/4" plywood that will be the countertops. I cut them out to fit the overall layout as per the wall measurements. Where there's a break in countertops like for a slide in stove, I'll cut a filler top for the spacing. Brown paper could be used in place of a panel. But I find maneuvering the paper layout and fitting cabinets to it pretty much destroys it.
Then I lay out the tops and draw right on the tops the base cabinets as they go. I also draw right on the tops the upper cabinets, as they go. Doing this accomplishes several things. When I say draw, it's not just the outside lines for the carcasses, but the actual thickness of the carcase walls. That way, the planning for the joinery and figuring the finished ends can be done. If dadoes and rabbets or whatever joinery methods are being used, it will give the exact size of all the parts.
This method will also solve all clearance and fitting situations. If the countertop pieces are cut exactly to the needed wall dimensions, and everything above and below it is drawn to fit, they most likely will fit. Any filler pieces can be easily figured out.
With this done, you have the whole kitchen laid out, and all the sizes of all the pieces needed can be transcribed to lists for figuring materials, cut lists, and possibly an order for a sequence of assembly. For shops with limited space, once the boxes go together, space becomes a premium.
With everything detailed, an accurate materials list, cut list, and layout sketch can be made. All the parts can be numbered or lettered and transferred to the list, and that way, you'll know what is cut what isn't, and in the end if anything is missing. Parts marked that way won't get used for anything other than what they are intended. I like to make several copies of all the wall elevation drawings. They don't even have to be to scale. Right on one set titled "cabinets" will be all the numbers or letters for the boxes, another set titled "doors and drawer fronts" will have door and drawer front numbers or letters, and likewise for shelves. The drawers are also marked. With these drawings, at any time during the project, I know what part is what, and where it goes. These drawings help in making the cut list, and as parts are cut, they just get marked and checked off.
Once all the boxes are assembled, they should fit right on the countertop drawing. If elevation drawings are made, all the marked parts, such as door and drawer front numbers or letters will match the actual parts.
For layouts other than kitchens, that don't utilize a countertop per se, a mock panel to represent the overall depth and width can be used, and then in plan (view), the drawing can be done. For working out elevation details, they can be drawn out full size on brown paper.
Those drawings, and lists with all the parts will tell you what and where everything goes even before you turn on the saw.