Basically, it is better to mix HASL module counters with the core nationality counters.
Otherwise, you will eventually be burdened with too many duplicates of storage systems for too many HASLs. They usually also contain some (more) of the standard units and vehicles. Furthermore, there may be a few scenarios you play that require more units of a given type than are part of the core module countermix (if so, this usually means certain vehicles). Or some scenarios require counters that were published in HASLs (for example German 447 SS Squads).
My advice would be the following:
When you organize your counter storage, really think long term. Keep in mind which counters you might need for 'regular' scenarios in the future after you have been able to aquire the HASLs they come with and leave the respective slots in your storage system empty for now but do incorporate the types into your system. That way you will be able to avoid most reorganizing of your storage solution when your collection of counters grows over the years. This will save you a lot of work - and not unlikely money, too, as typically players start with an 'imperfect' storage solution that they totally redo/relabel after a couple of years including buying new storage containers.
What I would aim at is going for a storage solution that can hold basically a 'double OoB'. This would mean for example 52 squads of a given type. For AFV/Guns you have to look: Sometimes you get 6, 4, 3 or 2 in a Core module. In my set, I tried to accumulate them up to 6 per type with going up to 12 for some few very common ones (for example German 251/1 half-tracks or some variants of the Pz IV or Sherman or T-34). The counter for this, I took from the core modules I have, SKs or HASLs. That should allow you to cover all but the very largest Campaign Games.
Furthermore, I have taken to the habit not even to punch any counters of which I have already reached the 'limit' for my set. In case I really want to play a certain CG that require counters that don't have punched yet, I can still do it then.
For my storage, I use RAACO. If you should be interested in details that not only pertain to RAACO storage but how to tackle it in general, see this link:
Another great site for inspiration for various storage solutions (RAACO, Plano, and others) can be found in the download-section of the Texas ASL Club website: