Both "are you lying" and "I am lying on my bed" are correct, and yes, the pronunciation is the same for both words in this case.
However, the past tense and the past participle inflections in English verbs can can be very confusing to English learners at times.
The following are the examples of the verb inflections that could be confusing in their present, present progressive, past, and past participle forms:
To recline: lie, (am) lying, lay, (have) lain
I want to lie on the bed and rest for a minute. -- present tense
To tell something not true: lie, (am) lying, lied, (have) lied
Are you lying to me? (Are you telling a lie?) -- present progressive
I am sorry, I lied to you yesterday. (I told a lie to you yesterday.) -- past tense
A bird lays eggs; or to put something in a particular position: lay, (am) laying, laid, (have) laid
A hen lays eggs. -- present tense
The mother laid the baby down gently on the bed. -- past tense
I hope the above information helps.