Your understanding is incorrect. You can have multiple copies of a spell active and functional, but any bonuses they apply won't stack unless they are dodge bonuses (or unnamed, circumstance, or racial provided they count as coming from different sources). You are probably thinking of the following rule section:
Spells that provide bonuses or penalties on attack rolls, damage rolls, saving throws, and other attributes usually do not stack with themselves. More generally, two bonuses of the same type don’t stack even if they come from different spells (or from effects other than spells; see Bonus Types, above).
(from Combining Magic Effects)
That section of the rules tries to explain, in general terms, what happens when you apply multiple spells at once. That's why it uses terms like 'usually', 'most', etc to qualify it's descriptions, so that it's clear they aren't rules that spells need to explicitly make exceptions for so much as general defaults helpful to understand how the system works. There is one annoying exception, though, if you play a strict RAW game:
Same Effect More than Once in Different Strengths
In cases when two or more identical spells are operating in the same area or on the same target, but at different strengths, only the one with the highest strength applies.
This one section fails to qualify itself as not actually a rule, and is inconsistent with the behavior of the system without it, which makes it efficacious at changing the system. According to this, only multiple identical spells with differing strengths are subject to a blanket non-stacking regulation. If the identical spells have the same strength, they apply normally. Strength is, of course, not clearly defined-- because the rule is in a section of broad advice and descriptive text, and is probably not intended to be a rule-- but, in any case, multiple castings of the same spell at the same CL from the same spell slot level in the same environmental conditions under the same buffs will have the same 'strength' by any reasonable metric, and that's generally what happens when you cast the same spell multiple times.
Named Bullet does not provide any bonuses to anything. It causes a weapon to deal extra damage when used; it does not provide a bonus to a weapon's damage roll. Multiple castings of Named Bullet have a cumulative effect, as do multiple castings of Greater Named Bullet, and they combine without issue.