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You can crate separate groups - then group them together.
Group is like any other graphic object - can be grouped with other objects.
Unless I'm missing something?
And I've regrouped everything - doing drag&drop in the Layers pallet:
First, a digression that will make sense in a bit. As fas as programming language design, there are those like Pascal or Modula-2 that were designed to be "self-commenting." That means that when you go back a year later to try to figure out how to tweak your program, it's pretty easy. Then, there are languages like APL that are designed for getting the job done quickly and screw the commenting. And when you try to go back a year later and tweak and reuse the code? You realize why some people called APL a "write-only" language.
OK, so in my textbook I did some text-heavy flowcharts for triage systems in InDesign rather than Illustrator. And I wanted to tweak them. And I realized that, when I looked at them in the Layers Panel, they looked a lot like APL code. So I decided to clean them up, to basically change them from APL to Modula-2 or Pascal. (I would tell you how long it is taking me but I would be very embarrassed.)
One of the things that occur frequently in flowcharts are lines with an arrowhead and the word "Yes" or "No" attached to them. Of course in my original, each line and word "Yes" or "No" were not grouped together. So, in the picture below, I'm trying to group the word "Yes" and it's line together. I've selected both of them. But, presumably because they're both already in a Group, I can't group them together in a subgroup: the menu item "Group" is grayed out. (Right-clicking won't work either.) I did figure out, eventually, that I can just drag them out of the group to where they're right under the top Layer in the Layers panel and then group them, no need for Dummy Objects.
 
But it's possible to UNGROUP objects that are grouped and are part of the group - without the need to ugroup everything - or moving this group out of the group and back:
Here's why I was perseverating about this. I will not tell you how long it took me to make this in a way that (a was true to the original, b) pleasing to the eye, c) easy to understand, and d) easy to tweak or adapt for a new or changed triage system. At least that's what I'm telling myself.
Final result:
Layers Panel, collapsed:
 Layers Panel, expanded:
I hope that at least one other person finds this helpful. And if you're wondering how I made the diamonds for the flowchart without moving over to Illustrator:
 
Each diamond is a Groupof two text frames, one to hold the actual text in the diamond, the other to form the diamond.
1. Create a square frame.
2. Give it a one-pixel border
3. Object > Transform > Rotate 45 degrees
4. Object > Transform > Scale > [unlink X and Y scaling] > Scale Y to 50%
 
Seeing and hopefully understanding correctly what you're trying to accomplish, I think it might be impossible or at least unfavorable to get a grip on creating, selecting, and editing elements quickly, based on Groups and Layers. These are hierarchically/physically very strict ! And it's visually not much more than a simple stacking order, in which only parent pages and masks can perform some exclusive side steps, but not with the ease of use you'd prefer or need.
You need style tagging, so you can control any visual expression and functional feature without messing with or within these Layers and Groups their hierarchical construction. Object Styles might help with that a lot ! Even the diamonds can be created, edited, and managed as one single text frame with an Object style ! They can define all visual and functional properties of any object, not just a simple Line and Fill setting. 
To create the "Negative Decision" object style, I used Corner Options to create the diamond shape, I used Vertical Alignment to center the text in de middle and add some inset, I connected it to a Paragraph Style to make the text the right font, white, horizontally centered, etc. I even restricted its Width to a set size, leaving the Height to whatever is necessary, and set it to always be Positioned left-aligned at 0mm from the right margin.
It takes a while and some thinking and discipline to set them up, but editing the size and appearance of objects will become just a matter of applying or Redefining their associated styles. Leaving Layers and Groups to control all objects their visual stacking, selecting, and relating.
Keep in mind to name styles semantically. E.g. not "Black Diamond with White Text" but i.e. "Negative Decision". So when you need to edit or overhaul a style its appearance, its name still makes sense. And of course, you can always override any setting or or even disconnect any style locally/manually.
[...]
Each diamond is a Groupof two text frames, one to hold the actual text in the diamond, the other to form the diamond.
1. Create a square frame.
2. Give it a one-pixel border
3. Object > Transform > Rotate 45 degrees
4. Object > Transform > Scale > [unlink X and Y scaling] > Scale Y to 50% 
By @keithconover
But you can do this as a ONE TextFrame:
1) create TextFrame - can be square,
2) type text,
3) use DIRECT SELECTION TOOL to select all PathPoints - you can do an area selection of the whole object,
4) set angle - 45 degree,
5) RESIZE - not scale - the TextFrame any way you want - by dragging any bottom - to make it a diamond.
6) apply ObjectStyle - this step can be made at any point - but not before 1) ;).
This way - it's still a fully functional TextFrame - where only the path defining it's shape is rotated - text / contents remains unaffected.
Well, I tried something like your method, and ran into an unexpected problem. The one thing I didn't do as you suggested was that I did scale, using x=0 and y=50, to get the exact right shape. I don't know, maybe that's the problem but I don't think so.
With my method of two text boxes, I was able to over-fill some of the diamonds, and with the single text frame, even though I tried to over-fill the diamonds (which I need for this flowchart), I was unable to figure out how to do this. See the picture: my original two-text-frame version on the top, the version done sort of like you suggested on the bottom. I tried setting the inset to a negative value but InDesign wouldn't let me. Sigh.
 
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