Can i make an application to start run when windows opens? without put program in start up list.

Because computers are freezed and there is no point to put it in start up list,
there are 2 HD, main partion is freezed were is and OS, and 2nd is small partition for storing datas....

so, if i store my program, .exe file in 2nd partition then after rr will not be deleted but how to make it run ...