I have two late 2013 iMacs - one with 3TB Fusion, the other with pure Flash. In day-to-day use it's very hard to tell the two apart, performance-wise (yeah, I could benchmark...). I think trying to out-smart a computer-managed cache is a pointless exercise, unless you design caches for a living (I don't).
I have one, concrete recommendation for you: Unless you need more than 2 TB of storage, try running on that internal Fusion alone for a while, and see how it works. I think you may be surprised at how well it does the job. I'd put OS, all apps, and any regularly-accessed data on the internal Fusion, infrequently-accessed data on the external. I know, this may completely waste the potential of that external SSD...
Now, it may turn out that configuring the external SSD as the boot drive with OS and apps, and the internal Fusion for "slow" storage may work even better - in theory the Thunderbolt interface shouldn't slow things down. HOWEVER, if that external SSD is a SATA drive, it's at a permanent speed disadvantage to the Flash portion of the Fusion drive. Would you rather have your apps and data in Flash, or SATA? The internal "slower" Fusion Drive could turn out to be faster than the external SSD in practical use.
As of today, you cannot use an external drive for Fusion. Otherwise, it might be potentially cool to fuse that external 500 GB SSD with the 2 TB HDD (then again, if it's a SATA drive, maybe it won't be so cool). I think Apple is smart to not provide the capability. Running a boot drive off of external is scary enough (been there, done that, hate the idea that "tripping" over an external wire/pulling the wrong cable can bring down the machine), but breaking a Fusion drive that way is even more perilous, as your data is spread, non-redundantly, across multiple drives. (Backup is even more essential with Fusion than with conventional drives.)
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When folks here discuss Fusion, I see many misconceptions about how these things work. Most important, for these purposes... Fusion works with blocks of data/code, not entire files, folders, apps, libraries, etc., essentially the same way blocks are read/written to/from RAM.
The folder/file/library metaphors constantly trip us up in regard to Fusion. If we were managing a split SSD/HDD configuration manually, we would have to deal with entire apps and data structures (like Photos and iMovie libraries), so we may think in those terms when we imagine how Fusion works (all 4.04 GB of FCPX, or my entire 365 GB Photos library being moved from HDD to Flash). However, the OS, apps, and even individual data "files" are highly modular under the hood - files and folders protected within a "package" (folder with special properties). We can't easily break those pieces up and divide them between HDD and Flash, but the OS can, and does, under Fusion. Unused portions of apps and OS live on HDD, so more data lives on Flash drive.
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Fishrrman and I always disagree about the performance of Fusion. The only thing true about his assertion, in my opinion, is that anything he stores in Flash will, naturally, perform at full Flash speed.
He constantly ignores the fact that everything on the HDD can perform only at HDD speeds, as if data or less-frequently used apps do not benefit at all from faster storage. Perhaps he only plays streaming media from his HDD. In that case, yes, there's no real benefit - read once from HDD, and it's gone. Perhaps he has so much RAM that there are no further reads from HDD after he opens a data file.
My Fusion Drive has 128GB Flash. That's as much Flash as an entire base model MacBook Air. The vast majority of the code and data I work with on a daily basis resides in Flash, automatically. Therefore, most of the time, I pay no "penalty" at all. If I shut down my system and start it up tomorrow, whatever data I was working on today (and probably for many weeks into the past) is still going to be in Flash. I only pay a speed penalty when code/data is brought in from HDD or the cloud, and that's a one-time penalty, since afterwards, it's in Flash, automatically. I have a 365 GB Photos library that opens, if you excuse the expression, in a flash (because the entire library doesn't have to be Flash-resident to open quickly). The far smaller Photos library on my father's newer, all-HDD iMac doesn't open nearly as fast.
Fusion is not about achieving maximum, theoretical performance from only those items that reside in a limited amount of Flash. It's about using Flash and caching to greatly improve the performance of a large, lower-cost HDD. If that premise didn't work, then no argument. In my experience, it works beautifully. With no management. No, "I'm running out of Flash storage, what should I move to the HDD?" Further, it uses all 128 GB of that Flash to my advantage. If, say, OS and apps occupied 64 GB of the Flash drive, would I then spend time figuring out how to exactly fill the remaining 64 GB, or might I leave part of that 64 GB unused, for overhead? I likely have far more stuff operating at Flash speeds than I'd every have by managing it manually.
It's a whole lot like the stick shift vs. automatic transmission debate. Driving stick shift can be fun at times, and if you're good at it, you can get up to highway speeds more efficiently than with an automatic transmission. But it's quite a chore in stop-and-go traffic and general urban/suburban driving. I drove stick for decades but currently drive an automatic (Honda Civic). I'm really pleased with the performance of today's automatics - no significant gas mileage penalty, very responsive... overall, a pleasure to drive, even when accelerating to highway speeds.
