You can use the LR Collections to sort batches of photos (they also stay in the main Library/Folders. I've used Collections taking a coupe approaches: in one "main" folders I'll put the folders of the working shoot, so that will reflect your entire Shoots folder. But I'll also create and use "special" Collection folders where I can browse subjects that interest me that would contain either a sub-group of a bigger shoot, or can contain groups from a number of shoots bunched together, so that in one look I see for example all the mountain landscapes the I've shot over the years, collected together, without have to search the whole dang file system!
Another great tool that is very useful and in fact important when dealing with a lot of photos is the Keywording tool. Say you are looking at a shoot with different select subject that you will want to revisit without having to sort through all in a batch. Suppose I had groups of Cityscape photos, some from Seattle, WA, some from Portland, OR, some from Los Angeles, CA...that kind of scenario. I would of course use Collections and could likely do fine. However, Keywords are a very effective tool -- You could have a "Master group" or "CityScapes" but you can apply actual keyword like "Los Angeles CityScapes" to the individual photos.
To go a step further and answering your concern about having to select/work on the photos one at a time, well, using the LR Select tool, in the Library Film strip it's easy to scroll through a shoot folder (or Collection), quickly selecting a batch of photos of interest, and then either put them in a Collection, or open the Keyword list/panel, and then create a keyword that is added to the whole selected batch!
One nice and important thing about keywords is that they show up out of Lightroom - Export a batch of jpegs with keywords "attached" (in the file Exif) and you can search for those keywords in "Normal" browsers/alternative apps, although if you want to prevent public asset to those keywords, you can Export the files with the Exif (including keywords) removed, although they still show up in your personal LR Library!