This link which you also mentioned describes the necessary steps to compile OpenCV on your machine. The version of OpenCV you install this way will be newer than the one installed with the ROS package, they usually have some delay. (Maybe not with Fuerte.)
Using multiple versions of the same library on a machine might cause problems with linking and it will create a bit of headache for you so I would avoid it.
Try running pkg-config opencv --libs to see if the ROS version pulled by Fuerte is available and you can use this with your projects later on.
For a starter IDE I would recommend Qt Creator. The easy way to set OpenCV up with your project in Qt Creator is the following:
Create a project
Open the .pro file of the project
Run pkg-config opencv --cflags
Add this to the .pro file: INCLUDEPATH += __result__of__above
pkg-config opencv --libs
Add this to the .pro file: LIBS += __result__of__above
In the end what you add should look something like this:
INCLUDEPATH += -I/opt/ros/fuerte/include
LIBS += -L/opt/ros/fuerte/lib -lopencv_calib3d -lopencv_contrib -lopencv_core -lopencv_features2d -lopencv_flann -lopencv_gpu -lopencv_highgui -lopencv_imgproc -lopencv_legacy -lopencv_ml -lopencv_nonfree -lopencv_objdetect -lopencv_photo -lopencv_stitching -lopencv_ts -lopencv_video -lopencv_videostab
脚本
https://github.com/wzyuliyang/Install-OpenCV/blob/master/Ubuntu/2.4/opencv2_4_9.sh