drill and tool table questions

Hi. I changed to the new linuxcnc2.5 from EMC2 just this weekend. I never had an issue with the old EMC setup.
My problem is this:
I use pcb-gcode to get my etch and drill g-code. I have setup the tool table in that ULP to match my drill bits. The output is acceptable.
I have formatted the tool table in linuxcnc to look exactly like my tool table in my ULP (which spits out the g-code i need)
problem is that when axis prompts me to change to tool 1(or any tool), tool 1 (or any tool) in axis is not tool 1 from the gcode. Is there some way I am not configuring it correctly?
I have seen where someone maybe cleared out the axis tool.tbl and just used the gcode. Is the output gcode from pcb-gcode ULP accepted by axis or am i thinking about this all wrong?
I would just like to be able to have axis tell me change to tool 1, then change to tool 4, then change to tool 8 (or whatever tools is required).
Any suggestions?
Can I provide any more info to make my explanation more clear?

Here is an example of the g-code output from pcb-gcode:snip to next tool:and so on with the different size tools

I see. Well I suppose the resolution I am looking for may be found with the pcb-gcode, ULP devs. If I understand correctly, I either need to manually change the g-code that the ULP creates for me or somehow change the source in the ULP so that it generates the correct code flow? Either way, once that happens will Axis use the generated drill file if it's formatted correctly (by deleting the Axis tool.tbl)? Or will I have to have Axis tool table to match my ULP tool table?
I apologize if none of this belongs here and I should be somewhere else asking these questions. When I first started I swear everything was plug and play and now that I upgraded I am having to set things that I either never had to or forgot how to .
Thanks for your help!