It’s often a pain to get a book published when it’s by a first-time author. With nepotism, elitism and favouritism ruling rampant in the publishing houses, new authors are often at a loss after being casually dismissed and shunted out on their faces by snooty publishers. Considering the bleak state of affairs, more and more amateur authors are seeking the service of eBook publishers online. E-publishers give out good promises about publishing and distributing the books for a certain amount of fee (which is in many cases, much less than the exorbitant fees charged by big publishing houses). But before one takes up the offer of any such eBook publisher, they must be sure about a few things:

The Nature of the Service:
eBook formatting and publishing services which are marketed to authors on a direct basis should be non-exclusive. They must not impose any clause about not being able to sell your book through any other publishing medium while your contract with them is on.
(Note: Kindle Select of Amazon and Apple iBooks are exceptions)

In Case it is Exclusive, You Have to Have a Thorough Understanding of the Clauses:
First, flesh out a contract with clear and easily identifiable clauses. In most cases, the duration of the contract would be for, say, 70 or more days; though it could be longer if you’re working through an agent. But seeing as how the market for e-books fluctuates rapidly, it would not be advisable to remain in the contract for more than two years.  

Make Sure That You Control the Price:
It is more or less a standard practise in the e-Book publishing industry to allow the author complete control over the pricing. So, this is something you will have to make sure is mentioned clearly in the contract, lest you are duped by some fraudulent publishing house.
However, you must be warned that no publishing house would permit you to offer your e-books on sale on other sites. Amazon specially, is very strict about such things and would not allow its authors to market their ware at lower prices elsewhere. In case an author is found doing so, their books will automatically be marked at lower rates on Amazon. If you provide your net-book for free anywhere, Amazon would promptly make the Kindle Edition free as well.

The Way the Royalty is Calculated:
The publishing house should have an upfront and transparent policy on the issue of royalty. So scan the agreement very carefully to see the cut-off for the commission that you would be charged by the online publisher. Make sure not to price your book too low or you’d be left with nothing, even if a paltry 20% is cut in terms of commission.