What you name your formations and how many levels you have in your Ground OOB is entirely up to you. Most people use the standard military nomenclature to make things easier for them but Aurora lets you RP your armies any way you want.
What sizes to use is also absolutely free but many - if not most - players use the Troop Transport bays as a guideline, especially at the bottom rungs, so that your lowest level formation is either 5,000 tons or 25,000 tons. Going under 5,000 is detrimental against spoilers and NPRs as it means that the enemy will get more than usual number of breakthrough attacks due to wiping out an entire formation. I and few others tested this back when C# came out but this effect is really noticeable only when the difference in formation size gets towards the extreme end of the spectrum. Commander bonuses and especially tech level differences are easily more important than formation size.
But another thing to keep in mind is that if your smallest formation is 5,000 tons, you are going to need a ton of commanders to lead all those formations and their parent formations and so on. Unless you invest heavily in academies, you won't have enough commanders to go around, especially good commanders, which negates the mechanical reason to use an intricate command structure - multiplying commander bonuses from level to level.
Remember that individual units, entire elements and whole formations can be drag & dropped in the OOB window so modifying your OOB is very much possible and relatively simple too. It's not something to get too worried about. It's generally best to start from the bottom and build up as your armies, capacity and knowledge increases. For example:
Offensive Group - 25,000 tons - vehicles with a lot of CAP, HCAP and some MAV and LAC
Defensive Group - 25,000 tons - infantry and static units, roughly similar composition
Command Group - 25,000 tons - vehicles and static, has MB, CON (the latter especially can take a lot of space, don't skimp on them) and LOG
Make sure both OG and DG have a HQ capable of commanding 25,000 tons and CG has a HQ capable of 125,000 tons. Then build two OG, two DG and one CG. Once they are built, drag the OG and DG over the CG to form a 2-layer OOB. Build a troop transport that can move 125,000 tons. Now you have an expeditionary force that can both attack and defend depending on enemy numbers, can entrench itself thanks to the CON units and has enough supplies in the LOG units to keep fighting for at least a month.
Now, this isn't an optimised build by any means but it will suffice you for fighting certain spoilers and NPR outposts and such.