Normally you don't need to open different instances of Matlab but you can use the Parallel Computing Toolbox which runs instances in parallel only as much as is necessary. There are many alternatives depending on your needs, from parfor up to running independent processes on different workers in the background.
If instead you want to open independent sessions manually you have to consider that on an x64 Windows machine you will occupy about 2 Gb of ram for each execution, without considering the workload that depends on your code so it could be even much more. Core assignment is automatic and depends only on the drivers and not on Matlab, so everything happens at the lowest level as if you were opening 2 different programs in multitasking.
