What is the best manner in distributing the meat of the Aqeeqah?

It is better to divide all of it as cooked meat amongst the poor and the needy. Dividing it into three portions is a Sunnah, but it is permissible to keep all of it provided that a portion, even a small one, is given to the poor and needy(one kilo for example).

What should a person, who delayed making up missed fasts of last Ramadhaan due to the continuance of the same excuse, do?

It is permissible for one, whose excuse for not making up missed fasts of last Ramadhaan has continued, to delay fasting until the excuse ceases to exist, and he is considered neither sinful, nor obligated to pay a ransom.

Does the deceased hear the supplications or recitations of those visiting his/her grave? And does making constant supplications for the deceased who didn`t adhere to performing the prescribed prayers ameliorate his/her affliction?

Praise be to Allah the Lord of the Worlds.

In principle, the dead hear the living since it has been rigorously authenticated that the Prophet (peace and blessings be upon him) ordered the bodies of the idolaters slain in the Battle of Badr to be buried. He then approached them and called them one by one and said, “Have you found what your Lord promised to be true for we have found what our Lord promised us to be true.” ‘Umar asked him, “O messenger of God! Why do you speak to lifeless bodies?” The Prophet (peace and blessings be upon him) replied, “By the One Who has sent me with the truth! You do not hear my words better than they do except that they cannot respond.”{Related by Bukhari & Muslim}.

However, not all the deceased are in the same situation because Allah the Almighty says, "Before them is a Partition till the Day they are raised up."{Al-Mu`minun, 100}. Moreover, supplication reaches the deceased. And Allah knows best.

Is Aqeeqah due on the miscarried embryo?

No Aqeeqah is due on the dead embryo.