Significance of putting tulsai/ flower
Tulsi has the greater capacity to absorb and emit sattvik and Krushnatattva frequencies present in the universe. Therefore use of tulsi while offering naivedya imparts two benefits.
The tulsi leaf used while offering naivedya absorbs the subtle frequencies emitted from the food. When this tulsi leaf is offered to the deity, the deity principle rapidly absorbs the frequencies present in the leaf.
There is subtle covering of raja-tama present in the atmosphere around the food to be offered to the deity as naivedya. When a tulsi leaf is kept on the food, the sattvik frequencies emitted from the tulsi leaf reduces this covering. Besides the atmosphere around the plate or banana leaf meant for serving the naivedya gets purified. This retains the sattvikta of naivedya for a long period.
Thus the tulsi leaf is used for offering naivedya for receiving the grace of the deity by pleasing Him/Her. Therefore there is a rich tradition of offering prayerful obeisance to tulsi plant loved by Lord Vishnu every morning and evening as mark of gratitude because it is a destroyer of negative energies and a purifier of the atmosphere.
(Amritha Vahini - Google group)