Yes, it is a bit annoying but you can fix it with some links:
sudo ln -s /usr/local/bin/node /usr/bin/node
sudo ln -s /usr/local/lib/node /usr/lib/node
sudo ln -s /usr/local/bin/npm /usr/bin/npm
sudo ln -s /usr/local/bin/node-waf /usr/bin/node-waf
There might be more but that is all I have run across so far. Lack of node-waf will cause some npm installs to fail with a rather cryptic error message.