One thing that would improve this quite dramatically would be to separate out each activity into a self-contained method. You could then get a clearer picture of any common code which could be split out further into helper methods. Something like:
public static void withdrawal(int account type, int transaction, int amount) {
}
public static void deposit(int account type, int transaction, int amount) {
}
public static void main(String[] args) {
System.out.println("1.Deposit Money"+"\n2.Withdraw Money"+"\n3.Transfer Money"+"\n4.Quit");
int choice1 = in.nextInt();
System.out.println("1.Checking"+"\n2.Savings");
int choice2 = in.nextInt();
System.out.println("Enter amount");
int amount = in.nextInt();
switch(choice1)
{
case 1:
deposit(choice2, choice3, amount);
break;
...
}
}