One side of the rebate (or raggle) in stone should be deeper than the other. This allows the panel to be slotted in and then slid back into the shallower rebate. Which side the deep rebate is on is not important, but you must determine which is the deeper and its minimum depth all along the raggle.
Adjusting the placement of the panel
To help move the panel from side to side stiff oyster knives and lead knives are important. This allows you to get behind the edge and slide the panel to the side, especially when it is sitting on top of another panel to make the fine adjustments to get the lead lines flow correctly.
In some circumstances, especially when installing a single panel, it is necessary to bend the leaves of the lead toward the installation side. After placing the panel, you then fold the leaves out one at a time into the raggle slot.
Top and bottom rebates
For the top and bottom rebates it is important that the top is the deep one. You insert the panel up into the slot a the top and let it settle into the bottom rebate. The panel should be completely covered by the stone.
In all installations into stone, you should carry extra came of at least 12mm (1/2”) to solder round the panel when the stone work is not as accurate as it should be, either through workmanship or weathering.
Have some little blocks of wood and some whittling tool to hand to wedge the panel in till mortared. It is possible to use little scraps of lead for the purpose. These wedges don't need to be that robust, they are just there to hold the panel in place until the mortar is in.
Mortars for stone should be of lime cement, or sand mastic. Don't use silicon, you'll never get it out again! Also don't use putty as this stains some types of stone and the oils leech in to the stone, causing the putty to dry and therefore the window ceases to be watertight.