Printing 100 prime numbers
STOP. Do not use system("pause"). This is not portable. If you
haven't already, read
this
Stop using using namespace std. Read
this.
I mentioned this in your last review as well.
You don't need to use std::endl for every new line of your output
table. Doing so flushes the output stream needlessly.
You don't need two vectors. Just two for loops and one vector will
suffice. Take a look at the example below.
For beginner code, I think you have good documentation(comments).
Although for some people, it might err on the side of excessive.
You could have initialized the array with the first three primes.
That would have cut down the number of iterations. 

 long primes[MAX] = {2,3,5};
 int count(0);             // Count primes found



Example:


#include  &lt;iostream&gt;
#include &lt;vector&gt;
#include &lt;iomanip&gt;

using std::cin;
using std::cout;
using std::endl;
using std::setw;


int  main()
{
    int counter = 0;
    std::vector&lt;int&gt; primes;

    int N, output;
    cin &gt;&gt; N;
    output = N;
    for (int i=2; N &gt; 0; ++i)
    {
        bool  isPrime = true;
        for (int j=0; j &lt; primes.size(); ++j)  //First pass(i==2), will not enter second loop because size() == 0
        {
            if (i % primes[j] ==  0)
            {
                isPrime = false;
                break;
            }
        }

        if (isPrime)
        {
            primes.push_back(i);
            --N;
            cout  &lt;&lt;  i  &lt;&lt;  "\n";
        }
    }


    for(int i=0; i &lt; output; i++)
    {
        if (i % 5 == 0)      // For a new line on first line of output
            cout &lt;&lt; "\n";      // and on every fifth line that follows

        cout &lt;&lt; setw(10) &lt;&lt; primes[i];  // Provide space between numbers
    }
    cout &lt;&lt; endl;

    return  0;
}