fl8m said:increasing thier level just meant increasing the difficluty of encoutners or they get less xp
This isn't right at all.
Per RAW, 2 PCs will get twice as much XP each as a default 4-person party. So if you give them encounters EL 2 under Party Level they will get the exact same XP. Personally I'd suggest averaging encounters more like 3 or 4 under Party Level - they get 1/3 or 1/2 less XP than standard, but 3e's standard XP table awards so much XP anyway that that's unlikely to be a problem. And if it _is_ a problem just increase the XP awards you hand out! Maybe give full monster XP plus story/roleplay/goal XP on top. XP should _never_ be a problem, it's entirely in the hands of the GM unless you have a rotating GM system and an agreed XP mechanism. Even then it's easy to tweak.
I think your mistake is probably hitting them with encounters too high for their level.
Here's my guideline for you:
A 2 PC party has about 1/2 the offensive power of a 4 person party, but only about 1/4 the survivability because they lack defense in depth and the synergy effects of a good spread of classes. Thus a typical 2-man party should be treated as having Party Level roughly 3 under the actual character level of the PCs.
So a challenging encounter that's unlikely to kill PCs should be 3 ELs under Party Level. If you have 2 level 6 PCs, an EL 3 encounter like 1 Ogre or a Wight (both CR 3) will be a fair challenge. An EL 6 encounter (eg a troll) will use up 50% of party resources - in practice that could mean a dead PC - and so should be avoided except for critical combats.
Of course a 2 person party's capabilities are narrower than the standard party, and you need to use judgement in assessing CRs. A party of Cleric-6 + Wizard-6 will easily defeat a wight but might have trouble with an Ogre. A party of Ftr-6 plus Rogue-6 should handle the Ogre ok (unless the ogre crits the Rogue) but will be in severe danger from the wight.