The two things are entirely unrelated.
Regardless of any other levels you may have, the Minor/Major Magic Rogue Talents explicitly list how they work, how many times you can use them, etc.
A rogue with this talent gains the ability to cast a 0-level spell from the sorcerer/wizard spell list. This spell can be cast three times a day as a spell-like ability. The caster level for this ability is equal to the rogue’s level. The save DC for this spell is 10 + the rogue’s Intelligence modifier.
You gain that specific spell as a 3/day spell like ability that uses your rogue level as the caster level and uses a standard INT based DC.
If/when you gain levels in Wizard, these are entirely unaffected. You will gain spell casting as a Wizard, which will give you your selection of unlimited cantrips and first level spells to start, as prepared from a spell book.
As a side note...
If this is what you are going to have fun doing then do it, but it's worth noting that, generally speaking, a Rogue/Wizard multiclass is going to be a very underpowered character unless you've got some specific gimmick in mind.
A lot of people will look down on multiclassing in general very heavily, but the truth of the matter is that it can be done very well, and there are many very powerful multiclass builds, especially for PFS, since so many of the classes are very front-loaded, with all their best features coming in the first few levels.
That said, in this scenario, going from a martial class that is already widely regarded as among the weakest into a d6, half BAB caster is going to significantly hurt whatever it is you're trying to do.
As I led with, if this is what you're going to have fun doing then do it, but I think it's something you should put serious consideration into before locking yourself into something you may end up unhappy with.