Many sci-fi writers like to add alien languages to their manuscripts. This can help to add a lot of texture to the story, define some big differences between characters and provide opportunities for conflict.
But some questions are when to add an alien language, as well as how to do it properly.
I once knew an amateur writer who added monosyllabic, guttural sounds like 'grok' and 'blor' to his manuscript. Not very creative, especially as his alien race was supposed to be highly intelligent. A later attempt had him writing long, flowery alien prose full of wooshes and chirps. Better? Yes. But realistic? Hardly. His invented language completely lacked function or form.
In both the above examples, there was no structure. If the communication was only supposed to be a tiny bit of the story then that would have been fine. But it wasn't. His story (which never got picked up) was partially-based on the difficulty in translating communications between humans and aliens (for an excellent example on how to do this, pick up Story of your Life by Ted Chiang. His inclusion of the Sapir–Whorf hypothesis was absolute genius).
Even though an alien language is not real, it should be realistic. That means you need to take a number of things into consideration: you need to have nouns, verbs, some prepositions and at the very least a couple of conjunctions. Nouns can be anything, really. Look at English, for example - rock and stone mean pretty much the same thing in a particular context, but sound completely different. However, they can also convey different meanings. A rock can be viewed as either a large or a small object, and usually with an uneven surface, while a stone tends to be visualized as small and somewhat polished. Even differences in the perceptions of objects can further conflict in the story.
Starting off with verbs is always a good bet. Most importantly they need structure; infinitive forms and stems (or even prefixes! It's an alien language, after all. Look up the Klingon language). Walk, eat, sleep, fight, etc. are all good starts. After all, you're going to write an epic novel that will eventually get published and then turn into the next big thing, right? Once you create your infinitives (to run, to walk, to fight), then conjugate them. Prefixes or suffixes - it doesn’t matter. An excellent language to use as a pattern is Spanish, which has a very regular verb conjugation model. Spanish has three infinitive stems (ar, er and ir), and the stem will denote the type of conjugation for the 1st, 2nd and 3rd person conjugations, both singular and plural. You don't need to get into compound verbs with your alien language (i.e. I have written a letter, as opposed to I wrote a letter) unless you really want to go all out and do actual research. As we said before - keep it simple. By the way, 501 Spanish Verbs by Christopher Kendris, Ph.D. is an excellent reference for this popular (although not alien) language.
If you really want to go gangbusters, invent even more conjugations, such as a 4th person plural where it only refers to a certain caste of beings, and not others in the same vicinity/conversation.
The easiest way to add an alien language to your manuscript is to use the bracket method:
"[Please forgive me. I have not yet mastered your tongue]," said Max.
"[There is nothing to forgive, my friend. I find your accent to be quite refreshing]," Koji responded as he handed Max a cup of hot green tea.
The above example, extracted from LIVES OF LOST ANGELS, the second book in the VROL TRILOGY of THE PRĪMULĪ PROPHECIES, has a conversation between Max Gunnarsson and a noodle shop owner named Koji. The latter doesn't speak English, but Max speaks Japanese. I was pretty sure that if I had put actual katakana or hiragana script in my novel no one would have understood (except for Japanese readers, of course), so I made it so everyone could be a part of the storyline. Hence, the bracket method would work just as well with a multi-legged being from the Andromeda Galaxy who speaks in farts and whistles as it would with someone who speaks in a language written with non-Latin characters.
The bracket method can also be used to denote a lack of comprehension between two or more characters:
"My name is Bob."
"[This is a perversion! It communicates through its nutritional portal]."
Gender can be used in your alien language, or even a lack thereof. Perhaps your alien race (which we are to assume you have already detailed in your bible) has no gender and reproduces via parthenogenesis (development of an egg without fertilization). If this is the case they might not have he or she in their vocabulary. While this may sound limiting to some, it can actually add drama or conflict to the story line by making first contact all that much more difficult. Maybe your alien race has three genders (a la Ringworld's Pierson's Puppeteers, which have two male genders and a non-sentient, parasitized female host). Or perhaps the aliens have no sense of self - let's say a hive mind. Then they would only have two verb conjugations for each mood and tense - 1st person plural and 2nd person plural (we are and you (all) are). Also, unless you're an expert at languages, leave out the subjunctive form (regularly used in Spanish, but not so much in English.) Again, keep it simple.
Adding an alien (or even an Earth-based foreign) language can add a lot of realism to your manuscript if executed properly. Just start out with some research. You never know - you might come up with something so intriguing and well-done that you'll get picked up by a major publisher, become a best-seller and end up answering fan questions at ComiCon while watching people dressed like your characters walking around speaking to each other in your unique, invented language.
Now that would be cool.