You don't "put the A in Atá".
When the verb tá comes immediately after the relative particle a, they are combined. The relative particle a does not combine with other verbs, it usually lenites them.
cad a bhí sa mhála?
cad a bheidh agat?
cad a chosnaíonn sé?
cad a cheapann tú?
When you ask a question, for one: 'Conas atá sé?' vs. the statement, 'Tá sé micheart.'
Irish uses this 'a' to connect the 'question' word to the rest of the sentence, where English simply relies on the inverted word order.
'A' is used this way with other verbs as well: 'Cad a ólann siad,' for example (SatharnPH provides more examples above).
The word is also used in more idiomatic contexts: 'Is dúinn atá an bia,' for example, or 'is uisce a ólann sibh.'
It wouldn't be understood as "what did I miss?". But it also shouldn't be taken too literally - here are just a few examples from the NEID of os cionn meaning "over" or "above", rather that "over head":
"books were stacked on the table" - bhí leabhair carntha os cionn a chéile ar an mbord
"superimposed layers" - sraitheanna os cionn a chéile
"fines in excess of €1000" - fíneálacha os cionn €1000
"to marry above your station" - pósadh os cionn do chéimíochta
"half the population is above sixty" - tá leath an daonra os cionn seasca
"dawn broke over the hills" - d'éirigh an ghrian os cionn na gcnoc