As Felinius mentioned, the first example conveys disbelief. This is common with sentences that become questions, such as "you ate earlier" becoming "you ate earlier?". Contrast this to "did you eat earlier", which is plain.
The form "Will you be here?" is the inversion of "you will be here", which is the indicative, and is a very very common, plain way to form questions.
However, "you will be here?" is a sentence with a question mark, so is often used to express disbelief or surprise, among other things.
Check out Wikipedia's article on Questions, which calls these Polar Questions:
Different languages may use different mechanisms to distinguish polar ("yes-no") questions from declarative statements (in addition to the question mark). English is one of a small number of languages which use word order. Another example is French
And the following section on intonation:
In some languages, such as English, or Russian, a rising declarative is a sentence which is syntactically declarative but is understood as a question by the use of a rising intonation. For example, "You're not using this?"