This is quite complex.
Suppose I have two 3x3 matrices represented as squares on a grid. The squares have nine circles in them, at positions 1,1 ; 1,2 ; 1,3 ; 2,1 ; 2,2 ; 2,3 ; 3,1 ; 3,2 ; 3,3. Square A is located in the upper left corner, placed in such a way that its circle at position 3,3 intersects with the circle at 1,1 in Square B (located in the center of the grid.)
OK. Now, Square A will move towards the right until it reaches the stage at which its circle at 3,1 intersects with the circle of Square B at 1,3. Next, Square A will be shifted down so that points 2,1 and 3,1 on Square A intersect with points 1,3 and 2,3 on Square B, respectively. Now Square A will move all the way to the left until it reaches the stage at which points 2,3 and 3,3 on Square A intersect with points 1,1 and 2,1 on Square B, respectively. Once again, Square A will be moved down and it will shift towards the right, move down, etc. The process ends when Square A is located at the bottom right corner, its circle at point 1,1 intersecting with the circle at point 3,3 of Square B. In sum, Square A will follow a snake trail/zig-zag (from the left all the way to the right, down one unit, then all the way to the left, down one unit, then all the way to the right, etc.)

OK. In total, there are 81 intersections (3^4). 9 of those occur at Stage 1 (while it is moving to the right), 18 occur at Stage 2 (moving to the left), 27 occur at stage 3 (moving to the right once again), 18 at Stage 4, and finally 9 more at Stage 5.

I've begun to make a table that illustrates the concept. It maps the intersections of the points.

Square B / Square A

#.....Row...Col...Row...Col
----------------------------
01..... 1..... 1..... 3..... 3
02..... 1..... 1..... 3..... 2
03..... 1..... 2..... 3..... 3
04..... 1..... 1..... 3..... 1
05..... 1..... 2..... 3..... 2
06..... 1..... 3..... 3..... 3
07..... 1..... 2..... 3..... 1
08..... 1..... 3..... 3..... 2
09..... 1..... 3..... 3..... 1
10..... 1..... 3..... 2..... 1
11..... 2..... 3..... 3..... 1
12..... 2..... 2..... 1..... 3
13..... 2..... 1..... 1..... 2
14..... 2..... 2..... 3..... 2
15..... 2..... 2..... 3..... 1

(etc.)

Now, I would like to model this into a function... Actually, four functions. For example, I would like to supply the # and function 1 returns the SquareA.Row value; function 2 returns SquareA.Column value; function 3 returns SquareB.Row value; and function 4 returns SquareB.Column value.
NOTE: The table is just an example. I want the function to be modeled mathematically, and NOT based on the table. Basically I need to find the pattern...!

Can somebody help me?

I know that the way I explained all this makes it more complicated than it really is. Just try picturing in your mind how Square A moves about Square B.