The rapid advancement, use of diverse architectural features and introduction of High Level Synthesis (HLS) tools in FPGA technology have enhanced the capacity of data-level parallelism on a chip. A generic FPGA based HLS multiaccelerator system requires a microprocessor (master core) that manages memory and schedules accelerators. In a real environment, such HLS multi-accelerator systems do not give a perfect performance due to memory bandwidth issues. Thus, a system demands a memory manager and a scheduler that improves performance by managing and scheduling the multi-accelerator's memory access patterns efficiently. In this article, we propose the integration of an intelligent memory system and efficient scheduler in the HLS-based multi-accelerator environment called Advanced Multi-accelerator Controller (AMC). The AMC system is evaluated with memory intensive accelerators, High Performance Computing (HPC) applications and implemented and tested on a Xilinx Virtex-5 ML505 evaluation FPGA board. The performance of the system is compared against the microprocessorbased systems that have been integrated with the operating system. Results show that the AMC based HLS multi-accelerator system achieves 10.4x and 7x of speedup compared to the MicroBlaze and Intel Core based HLS multi-accelerator systems.