You have a lot of curley braces there... I've stripped out the likely harmful braces and given your code proper indentation. Corrected your loops and exit criteria.
You need to work on your formatting and tracking your opening and closing braces, brackets etc. It will make your code easier for others to follow and easier for you to debug. You do not put braces around EVERY section of code you separate. They should only be used in specific places.
class Main
{
public static void main (String[] args) throws IOException
{
Scanner scan = new Scanner(System.in);
int[] arrayone = new int[10000];
int[] arraytwo = new int[10000];
System.out.println("Enter integers ");
int userNumber;
for (int i = 0; i < arrayone.length; i++)
{
arrayone[i] = scan.nextInt();
if (arrayone[i] < 0)
{
break;
}
}
System.out.println("\nEnter the values for the second array, up to 10000 values, enter a negative number to quit");
for (int i=0; i<arraytwo.length; i++)
{
arraytwo[i] = scan.nextInt();
if (arraytwo[i] < 0)
{
break;
}
}
System.out.println("First Array:\n");
for (int i=0; i< arrayone.length; i++)
{
System.out.print(arrayone[i] + " ");
}
System.out.println("Second Array:\n");
for (int i=0; i< arraytwo.length; i++)
{
System.out.print(arraytwo[i] + " ");
}
}
}
I didn't do all the work for you but you should now be in a better place to solve the rest yourself.