Praise be to Allah.
If the building you describe was intended as a mosque, and the people on the higher and lower floors can hear the voice of the Imaam, then the prayer of all of them is valid. In this case it is not permissible for menstruating women to sit in the place that is prepared for prayer in the lower level, because it is part of the mosque. The Prophet (peace and blessings of Allaah be upon him) said:
“I do not make the mosque permissible for menstruating women and those in a state of ritual impurity.”
As for a menstruating woman passing through the mosque for some purpose, as long as she takes care to ensure that no blood leaks, then there is nothing wrong with this, because Allâh says (interpretation of the meaning):
“… Approach not As-Salaah (the prayer)… when you are in a state of Janaabah (i.e., when you are in a state of sexual impurity and have not yet taken a bath) except when travelling on the road (without enough water, or when passing through a mosque)…” [al-Nisa’ 4:43]
And it was reported that the Prophet SAWS (peace and blessings of Allaah be upon him) told ‘Aa’ishah to fetch his prayer rug from the mosque, and she said that she was menstruating. He SAWS (peace and blessings of Allaah be upon him) told her: “Your menstruation is not in your hand.”
But if it was not the intention of those who established this mosque that the lower floor was to be part of the mosque, but it was to be a storeroom or to serve some other purpose, as mentioned in the question, then it does not come under the rulings governing mosques. It is permissible for menstruating woman and those who are in a state of impurity to sit there. There is nothing wrong with praying there in the places that are pure (taahir) and are not part of the washrooms, as it is permissible to pray in all clean places where there is no shar’i reason not to pray. But anyone who prays there cannot be considered to be following the imaam who is praying on the upper floor, if he cannot see him or any of the people who are praying behind him, and because this is not a part of the mosque, according to the more correct scholarly opinion.
With regard to the pillars which interrupt the rows, they do not adversely affect the prayer, but if it is possible to form the rows in front of or behind the pillars so that the row will not be interrupted, this is better. And Allaah is the source of strength.