Lets assume the next example:
1. mkdir /export/home/tester/1
2. cd /export/home/tester/1
3. vi args.c
-----------------------------------------
#include <stdio.h>
#include <string.h>
#include <stdlib.h>

int main(int argc, char**argv) {
    int i;
    
    // Prints arguments
    printf("Arguments:\n");
    for (i = 0; i < argc; i++) {
        printf("%i: %s\n", i, argv[i]);
    }
    
    return 0;
}
-----------------------------------------

4. vi Makefile

---------------------------------
args: args.c
    gcc -g -o args args.c
----------------------------------

5. Start Netbeans
6. New project with existing Makefile
6.1 Project Name and Location set default(project location is ~/MakefileProject1)
6.2 Build actions: choose Working directory: /export/home/tester/1
Build command: make
Output file: args
6.3 On "Source File Folders" add /export/home/tester/1
Click Finish.
7. Build project
8. Find executable file 'args'. It is placed in working
dir(/export/home/tester/1/) not in project dir(~/MakefileProject1/). 

You can't run or debug the project because in all cases executable file is
sought in project dir