Due to increased embedded processing requirements, modern SoCs are becoming heterogeneous computing platforms by combining traditional processing units with custom reconfigurable hardware accelerators (HAs) on an FPGA fabric. However, efficiently managing such HAs in an embedded Linux environment involves handling Linux kernel source code and creating custom device drivers specific to a target platform, therefore negatively impacting development costs, portability and time-to-market. To address this issue, we present LEOSoC, a snap-on user-space manager for dynamically reconfigurable SoCs. Using LEOSoC does not require any specific version of the Linux kernel, nor to rebuild a custom driver for each new kernel release.LEOSoC consists of a base hardware system and a software layer which run on SoCs from various vendors. The system identifies the SoC on which it is running and auto-adapts its communication channels to the HAs accordingly. Furthermore, LEOSoC allows applications to partially or completely change the structure of the HAs at runtime without rebooting the system by leveraging the underlying SoC support for dynamic full/partial FPGA reconfiguration. The system has been tested on multiple commercial off the shelf (COTS) boards from different vendors, each one running different versions of Linux, therefore proving the real portability and usability of LEOSoC in a custom industrial design. Finally, we use a cloud detection algorithm for multispectral image processing as a showcase for LEOSoC's capabilities and performance.