1 Did you go to the store today?
2 You went to the store today?
3 今日、店{みせ}には行った(か)? (I took the liberty of adding は
)
(1) is a normal English question; you've been taught that (3) is the way to form normal questions in Japanese; so therefore, the equivalent of (1) in Japanese is (3), right? Then surely, you have the answer to your question already?
Maybe I can get closer to what's troubling you, though.
The questions you're asking in Japanese, such as (3), would normally be structured in English as (1) and not (2) -- yet the Japanese grammatical structure resembles (2) more closely than (1), since the word order doesn't change at all from an ordinary statement. This makes you want to look for a different structure, maybe one that is closer to (1) instead.
However, you can't hope for Japanese and English sentence structures to align in this way. Even though (3) seems to be structurally very similar to (2), it does not mean (2).
The sentence (2) in English sounds like it's seeking "confirmation", or is a surprised statement. To represent its equivalent in Japanese, you need to add の:
4 今日、店{みせ}に行ったの(か)?
This indicates that the speaker is seeking an explanation of some aspect of the context/environment (for instance, maybe he saw some shopping bags lying around in an unexpected place).
This question illustrates the dangers of attempting to directly compare Japanese and English sentence structures. When you realize that (3) looks similar to (2) and you start thinking about how to translate (2), you should consider that as its own problem, starting by asking yourself "what are the nuances of this sentence in English?", rather than assuming that (2) corresponds to (3) because it looks similar.