MS-DOS Prompt Short-Cut and VMM32

Using the short cut “MS-dos prompt” to exucte DOS TSR programs is limited to conventional memory. Modifying the config.sys to allow upper memory, will not help beause the vmm32 will use all the upper memory no matter how big it is.
Please tell me how to limit the vmm32 to only use the 3k conventional memory and at the same time be able to use the upper memory from within windows DOS prompt.