If you have a reference to each Panel control use those and skip the first two lines of the code below (ie. the GetControlFromPosition() function I've used below to get the reference to the Controls) -
Control ctr1 = tableLayoutPanel1.GetControlFromPosition(0, 0);
Control ctr2 = tableLayoutPanel1.GetControlFromPosition(1, 1);
tableLayoutPanel1.SetCellPosition(ctr1, new TableLayoutPanelCellPosition(1, 1));
tableLayoutPanel1.SetCellPosition(ctr2, new TableLayoutPanelCellPosition(0, 0));
Replace the 0's and 1's with Row and Column Index where you want to place the control..