Since atom-shell is using a different V8 version from the official node, you need to build native module against atom-shell's headers to use them.
You need to use node-gyp to compile native modules, you can install node-gyp via npm if you hadn't:
$ npm install -g node-gyp
First you need to check which node release atom-shell is carrying via process.version (at the time of writing it is v0.10.5), then you can configure and build native modules via following commands:
$ cd /path-to-module/
$ HOME=~/.atom-shell-gyp node-gyp rebuild --target=0.10.5 --arch=ia32 --dist-url=https://gh-contractor-zcbenz.s3.amazonaws.com/atom-shell/dist
The HOME=~/.atom-shell-gyp changes where to find development headers. The --target=0.10.5 is specifying node's version. The --dist-url=... specifies where to download the headers.
Use npm to build native modules
Under most circumstances you would want to use npm to install modules, if you're using npm >= v1.2.19 (because a patch is needed to make npm_config_disturl work) you can use following code to download and build native modules against atom-shell's headers:
export npm_config_disturl=https://gh-contractor-zcbenz.s3.amazonaws.com/atom-shell/dist
export npm_config_target=0.10.5
export npm_config_arch=ia32
HOME=~/.atom-shell-gyp npm install module-name