An example method of implementing an application for a hardware accelerator having a programmable device coupled to memory is disclosed. The method includes compiling source code of the application to generate logical circuit descriptions of kernel circuits; determining resource availability in a dynamic region of programmable logic of the programmable device, the dynamic region exclusive of a static region of the programmable logic programmed with a host interface configured to interface a computing system having the hardware accelerator; determining resource utilization by the kernel circuits in the dynamic region; determining fitting solutions of the kernel circuits within the dynamic region, each of the fitting solutions defining connectivity of the kernel circuits to banks of the memory; adding a memory subsystem to the application based on a selected fitting solution of the fitting solutions; and generating a kernel image configured to program the dynamic region to implement the kernel circuits and the memory subsystem.