Building up a hidden cable bike is little different than installing cables on an external cable bike...only difference is routing the cables through the frame.
So here are the three most popular methods of routing cables:
1. Most new framesets sold with hidden cables come with what look like long straws that are conduit for pushing the cable through the frame. A new hidden cable frameset will come with these straws installed and held in place with tape.
2. Use an old inner cable. Cables have spine to them and can be used to fish fresh cables through. Start in the entry port at the top of the downtube and push an old cable through to where it exists the BB. With a piece of tape...tie the fresh cable to the old cable and pull the fresh cable through the frame.
3. This method takes a simple small vacuum hose. Take a piece of string and start at the top of the downtube and push the string into the top port and into the down tube. The vacuum applied at the bottom of BB will suck the string through the downtube. Attach the fresh cable to the string and pull it through the downtube.

Same approach above applies to both sides of downtube...and through the drive side chain stay...and/or through the top tube for rear brake routing.

Here's a tip. A novice will invariably drop a long straw into the downtube. This is inevitable. Don't panic...they are easily retrieved and simple to reinstall as conduit to route a fresh inner cable.

Above is about all you need to know if you have basic cable installing skills. With Specialized bikes...best cable routing is called the California cross...google it if interested...whereby front and rear deraileur inner cables when routed are physically crossed inside the downtube.
Poor shifting is almost always associated with a poor set up.
Hope that helps.