If you have a tool that you use more often than others, then use that. Other than that you can use any pointer, or a marker that you wish. It need not be a tool as such.
When setting up my tool table, I used a corner of my cross slide as the marker, because it was easy to measure to and from, to the tips of the tools I put in the holder.
Set your homing with, as Hood says, offset positions, so that when you home the machine, your marker/pointer or tool 0, (whichever you are using) homes to position 0,0 i.e. I assume X0 is on the centreline, I have my Z0 on the chuck. The DRO's should all zero (machine co-ordinates)
Now place the tools in their relevant holder - and it does not need to be all the same holder - and measure with a set of digital calipers, the distance from your marker to the tool tip. This is your tool offset. You can move the table to a more convenient position to do this.
You can test the offsets by putting the tools in, and (as I am sure you know) typing in the tool number, bearing in mind for Mach Turn the Tool number is a four figure number eg. T0202 - (tool number 2 and offset 2) both pairs of numbers must be included. G0X0Z0 should then take the tool tip to your 0.0 position.
You can see why I use a seperate marker. In my case, the corner of the cross slide is always there and I can always measure to it, especially if the tool is one you do not use all that often, and you wish to check the offsets. If you use a tool in a holder as a marker, you have a lot more adding and subtracting to do to get the differences in length and position.
Like you I also have a centre drill holder at the back of the table. I have made holders for all my drills so they just slot into it to a set depth. X offset is always the same, of course, and the z offset brings then point of the drill to the centre of the chuck, just in the little space between the jaws. This makes any depths easy to calculate.