Delete the cSpell stuff completely - you must have copied this from something d20, since in Pathfinder, cSpell is calculated for you.
The index field +1 is the level the increase happens at (index="0" is level 1, index="1" is level 2, and so on).
The value field is the total number of increases that have been gained to that point.
So, for (2,3,5,6,8,9,10), use this:
<arrayval field="cMagLevTot" index="1" value="1"/>
<arrayval field="cMagLevTot" index="2" value="2"/>
<arrayval field="cMagLevTot" index="4" value="3"/>
<arrayval field="cMagLevTot" index="5" value="4"/>
<arrayval field="cMagLevTot" index="7" value="5"/>
<arrayval field="cMagLevTot" index="8" value="6"/>
<arrayval field="cMagLevTot" index="9" value="7"/>
I also highly recommend using the editor instead of editint the XML until you're very experienced at creating content for HeroLab. The additional magic levels array is much easier to understand when seen there, and there's an info mousover that tells you that index+1 = level.
You can open two copies of HL at once (as long as you're not in demo mode). So, open d20 in one copy and Pathfinder in the other. In the d20 editor, open whichever prestige class you're copying from, and in the Pathfinder editor, open the class you're working on.