The two one pound notes act as one of a series of symbols that remind Pip of his criminal associations from his youth, harking back to his act of helping Magwitch in the marshes and his own act of robbery in stealing food and a file for him so he could eat and remove his ball and chain. The two one pound notes occur in Chapter 10 when Pip and Joe are in the Jolly Bargeman with a stranger, who seems to pay lots of attention to Pip. Note his actions:
It was not a verbal remark, but a prodeeding in dumb show, and was pointedly addressed to me. He stirred his rum-and-water pointedly at me, and he tasted his rum-and-water pointedly at me. And he stirred it and he tasted it: not with a spoon that was brought to him, but with a file.
Pip recognises that this file is the one he stole and gave to Magwitch and thus recognises that this man knew Magwitch. At the end of the night, the man insists on giving Pip a "bright new shilling" for Pip to have as his "own" which he wraps in some paper. It is only when they arrive back home that they discover that the paper it is wrapped in is actually two one pound notes, described as follows:
Nothing less than two fat sweltering one-pound notes that seemed to have been on terms of the warmest intimacy with the cattle markets in the country.
Note how the description of these notes as "fat" and "sweltering" seems to convey the criminal associations that they have for Pip, and this image of his past that he is unable to escape re-appears again in Chapter 28 when he rides with two prisoners. He overhears one of them tell the other about being asked to take the two one pound notes to a boy in the marshes. The novel seems to suggest that sometimes we cannot escape our guilty past - in fact, it repeatedly returns to haunt us.
You can read about this in chapter 28. Pip was overhearding two convicts talk about a couple of one-pound notes. This is during one of his excursions back to his roots, a time wherein he visited the Three Jolly Bargemen. A time he sat on a carriage for quite some time en route and with two convicts. He heard them discussing "two one-pound notes." They discussed where they retrieved them, and Pip what they would do with them. Pip seemed to think he didn't know these convicts but the two one-pound notes discussion seemed to remind him of something. The fact that these men were convicts seems to be important too. It might have had something to do with a certain night when he was a young boy at the Three Jolly Bargemen when 2 one-pound notes seemed to be used by a man who stirred his drink with a file, or knife.