The unknown caddy is most likely the problem since you should get similar performance from the USB3 SSD as you would the internal SATA III SSD. Although some SSDs can be very slow even from respected name brands.
Is the external drive connected directly to the laptop?
Personally I would only use a USB3 adapter, drive dock/caddy, or enclosure that supports UASP for optimal performance. I always stick with trusted & respected brands that have been available for years....such as Plugable, StarTech, and OWC to name a few. And I usually go for products using the ASMedia USB chipset as well since they usually support UASP and tend to be more reliable in my experience although they may cost a bit more.
I never recommend partitioning any drives because people almost always realize much later that one or more partitions is too small. If your other OS were to be macOS 10.13+, then you could dual boot to the internal drive by installing macOS to another new APFS volume (acts like a partition without restricting storage space as long as you have enough storage for two operating system....you need to always have 20GB+ of Free storage space at all times), however, El Capitan is unable to use the APFS file system so this is not an option. You can install up to macOS 10.14 Mojave for 32 bit apps.
