I am doing a lot of 3D projects. I will have several Bit changes. I remove the top surface in the first run. When I go to change bits is there a way to see where the relative position of the original top of the wood was.

A lot of projects in which material? Wood/Metal/Plastic/Foam...
As you are removing top of entire material, you should reference your machine to the machine bed.
Also in your CAM you should set Z datum to the machine bed. Then you are trouble free regarding your 3D (2.5D ) projects.

I am doing a lot of 3D projects. I will have several Bit changes. I remove the top surface in the first run. When I go to change bits is there a way to see where the relative position of the original top of the wood was.

If your machine has an ATC (automatic tool changer), the height and height wear data in the tool table will automatically compensate for different tool lengths.

I have a manual tool change system, BUT my VFD spindle cylinder is adjustable z along the  clamp, so I find it easier to have a block (hardwood or Aluminum) where I ALWAYS set the tip of the tool to that constant height block by moving the cylinder up or down along the cylinder clamp after each tool change.

Some people edit the M6Start and M6Stop macros to have auto tool zero on a plate at the side of the machine after every tool change. IN THEORY, it is a very good idea but only for CNC milling machines but not CNC routers. CNC Routers usually have very short Z axis (3-5 inches), and router bits & drill bits used (unlike endmills) are of very different lengths. What is happening is when you change to a very short router bit, the z axis may be already too close the lower limit switch (or -ve soft limit) so your machine will stop working very soon.
Using fixed block to reference every bit tip height (and adjusting the VFD spindle cylinder up and down) allows a CNC router to always operate without tripping the lower Z axis limit ALL THE TIME.
YOU must still do the auto tool zero on the material surface ONCE when you start the program.