For the moment I've divided the questions into two sections, story and character. If you have any questions, don't hesitate to ask. I'll be happy to answer them.

How long will the Ceph story run? Does it have a definite ending?

Yes, it does have a definite ending but it will take a while to get there. My time-line is three years but, that far in advance, I have a habit of grossly underestimating the time it takes to get things done.

How far in the future does the story take place?

The sun is going nova and is at some point in the beginning of the red giant phase, so something more than 4 billion years. The entire surface of the earth is a desert and the oceans have boiled away, forming a thick cloud of vapour that's gradually bleeding off as the atmosphere escapes. It is a thoroughly dead planet. The probability of humans existing so far in the future is probably nil, but it's a comedy so it really doesn't matter all that much.

Where did the humans go? Why doesn't Ceph(a) know?

The future humans that Cepha knew left for a previously established and prosperous colony. She does know where they have gone, but doesn't want to be reunited with them in her current form. That's why she told Cephus that she doesn't know.

Why did the Ceph go back to Earth?

It was Cephus' idea to go back to Earth and Cepha agreed only to get him to stop bugging her about it. Once they arrived to find the computer down and the robots rampaging, Cepha was intent to stay and set things right. It's her strong sense of duty and order that forces her to fix things even though the Earth is merely a tomb and of little consequence.

Are those humans in those orange pods?

Yes, in sort of an undead state. I intend to explain this in the near future with a short comic of its own and a few backstory pages.

Why did the humans leave the robots on Earth?

The robots were left because they were obsolete and not worth the trouble it would take to transport them to the colonies. For sentimental reasons, they left them on to maintain the Earth as a sort of tomb. This should also be covered in the coming backstory pages.

Why do you call them Cephus and Cepha outside of the actual comic?

I attached Latin suffixes to their names because I was feeling clever one day and needed some way of differentiating them when talking or writing about them. Cephus being male, and Cepha being female. It hasn't come up in the comic because it hasn't been necessary.
Also, Ceph is singular but the Ceph is plural. Of course, going for Latin I could call them the Cephi...but people have already taken to using "the Ceph" so, nah.

What do the Ceph care about the Earth/earthlings anyway?

It's their job. Their alien race is interested in all forms of life and consider living planets "wildlife preserves." The Ceph were specifically designed to study humans, (though they have also taken the forms of other earth creatures). They don't have any strict non-interference rule because they understand that their very presence makes that impossible. Instead, the Ceph follow a simple rule: if you're going to interfere with humans, do it as a human (you can just imagine the way male Ceph interprets this rule). The ship, before it took the form of a ship, hid deep underground and relayed the information the Ceph gathered to the collective.

How long have the Ceph been on Earth?

I'd say the Silurian period would be the time when the aliens would take interest in our little planet. That was the age of cephalopods. Of course they wouldn't have been the Ceph back then. Ceph was a name given to them by humans, and it refers specifically to their human form.

Why did Ceph(a) get tentacles all of a sudden?

Both of the Ceph can morph, but only in a limited way. They can become either more human or alien. If they were designed in another form, for example a cat, then they could only morph between feline or alien. The Ceph can change their form to something other than human or alien with the ship's assistance, provided that the ship has some kind of record of whatever they would want to morph into. They could possibly morph from human to feline if they had previously been both and, if for some reason, the ship didn't remove the genetic instructions for the previous form. The other way they can morph is by changing sex...if they happen to be a creature that actually has a sex.
So why tentacles? Because as aliens they have tentacles. Why at that moment? (p.28) The Ceph sometimes lose control over their form when they lose control mentally--as in extreme stress, pain or pleasure.

If the ship is telepathic then why don't the Ceph seem to be?

They are, but it's been under-used and perhaps handled a little too subtly. The two Ceph don't communicate telepathically because Cepha really doesn't want to know what Cephus is thinking. Cephus showed the potential to engage the computer telepathically in page 25 and Cepha's mind became fully immersed in the computer later.

What is the Ceph's relationship with the ship?

Short answer: The ship is their "mom".
Long answer: They are actually a single entity with more than one body, and yet complete individuals. The Ceph are like smaller satellites of the "ship" and they are all a satellite of the larger alien collective.
As an example of their bond, if the ship got damaged, the Ceph would feel pain, but would not be damaged themselves. The Ceph often, but do not have to, share this bond. Cepha has created a barrier between herself and her brother.

If the ship is such an intelligent being, why does it cheat at cards?

I tend to think of the ship as the Ceph's mom and, like most moms, does really lame things to try to be "cool" and "hip" to its kids. In this case, it does human things that it really doesn't understand. Though it's obvious that it gets some amusement out of it.

The Ceph seem oddly mismatched. Does the ship have a sick sense of humor?

The short answer is "yes" and it goes something like this:
Cepha: Why did you make him?
Ship: To keep you sane.
Cepha: But he drives me nuts!
Ship: Exactly!
The long answer is much more complicated and will be dealt with later in the story.

Does Cephus have the mentality of a six year old?

It sure seems so, but keep in mind--that's pretty good for someone who's just been born. He will grow up some as the story progresses.