No real mistake Ash, the 2 words are quite often used when meaning the other - much like code and cypher.
Just to clarify, Species counterpoint is a very specific thing and is often used as a way of teaching what was/is considered 'good' writing. The point of studying species counterpoint is to develop knowledge and use of the rules of good counterpoint writing. Because of that, the rules must be strictly adhered to or the exercise of doing species counterpoint is pointless.
It can become quite complex purely because the more notes in the counterpoint, the more rules there are to follow because many more situations can arise. Therefore sticking to the rules can become a little tricky!
For a very brief introduciton into just some of the rules you must follow for strict species counterpoint, try here:
http://www.schenkerguide.com/species1.html (and the other species links)
For examples of more in depth rules for species counterpoint see here:
http://www.unh.edu/music/Counterpoint/2_2_Rules.htm (2nd species 2 part)
http://www.unh.edu/music/Counterpoint/2_3_Rules.htm (2nd species 3 part)
http://www.unh.edu/music/Counterpoint/3_2_Rules.htm (3rd species 2 part)
As far as books go, "Counterpoint in Composition - the study of voice leading" by Felix Salzer and Carl Schachter is very thorough. Here's the book index:
Introduction
Part 1. The Techniques of Elementary Counterpoint
1. Cantus Firmus and First Species
1. Cantus Firmus
2. Two-part Counterpoint, First Species
3. Three-part Counterpoint, First Species
2. Second Species
1. Two-part Counterpoint
2. Three-point Counterpoint
3. Third Species
1. Two-part Counterpoint
2. Three-part Counterpoint
3. Three Notes against One
4. Fourth Species
1. Two-part Counterpoint
2. Three-part Counterpoint
5. Fifth Species
1. Two-part Counterpoint
2. Three-part Counterpoint
Part 2. The Techniques of Prolonged Counterpoint
6. Counterpoint in Composition, I
1. The Direct Application of Species Counterpoint
2. Two Major Influences on Contrapuntal Texture
7. Counterpoint in Composition, II
1. Melodic-contrapuntal Prolongations
2. Counterpoint within Prolonged Chords
3. The Evolution of Dissonance
4. Repetition and Articulation
5. Harmonic Influences on Voice Leading
6. Chromaticism; Contrapuntal Leading-tone Chords
7. Octaves and Fifths
8. The Chorale
1. The Elements of Chorale Writing
2. Setting a Single Phrase
3. Setting Groups of Two or More Phrases
4. The Complete Chorale
9. Combined Species
1. Combination of Two Second Species
2. Combination of Second and Third Species
3. Combination of Second and Fourth Species
4. Combination of Third and Fourth Species
5. Combination of Two Fifth Species
6. Progressions from Combined Species in Composition
10. Voice-Leading Techniques in Historical Perspective (ca. 1450-ca. 1900)
Heinrich Schenker also wrote 2 books on Counterpoint which are very good but fairly hard to get hold of.
I was quite lucky because my history of music professor at music college was a singer with a special interest in counterpoint! Made it alot easier than learning it by myself out of a book