On the command line, when you use the gcc command, you can give it options, also referred to as flags or switches, by using -. For example, gcc -Wall file.c will compile file.c and link it into an executable called a.out and output any warnings the compiler sees (use of -Wall is good coding practice). In order to change the executable's name, you use the -o filename flag. So gcc -Wall -o exe file.c will create an executable called exe. For the c99 flag, you'd compile with gcc -Wall -o outfile -c99 infile.c. Check the man page for gcc (or Google) for more information, assuming you're on some version of Unix/Linux.
In Netbeans, there should be a dialog somewhere that lets you change the command used for compilation. I've never used this particular IDE for C/C++, just Java, but I know Visual Studio has it. Look in Project properties or Options, something like that.
As to malloc, it allows you to declare arrays of whatever length you want, but you have to free them once you're done with them with the free() function. Google for more information.