Amisa pooja for Buddha I know that we can make great Karma by offering Flowers,candles,incense,food,robes and other things for the Buddha statue thinking as if the Buddha is alive. 
But whenever I do offer these things my mind says "The Buddha is not there to receive this.And this is not the proper way to pay respect for the Buddha. The proper way is to try to be mindful and try to be free from the defilement in the mind." 
Am I cultivating bad thoughts by thinking this way? What is the proper way to think when we offer these things to the Buddha statue?
Both are ways to show respect for the Buddha. Offerings are a lesser way compared with the practice of Sila, Samadhi, and Panna, but you do not have to choose between the two. You can develop the path and also make offerings.

The best way to make offerings is to make your offering be endowed with the three factors you have control over. The Buddha once taught that there are six factors that affect the merit of an offering, three of which are determined by the giver's mind:


  "Monks, the lay woman Velukandaki, Nanda's mother, has established a
  donation endowed with six factors for the community of monks headed by
  Sariputta &amp; Moggallana.
  
  "And how is a donation endowed with six factors? There is the case
  where there are the three factors of the donor, the three factors of
  the recipients.
  
  "And which are the three factors of the donor? There is the case where
  the donor, before giving, is glad; while giving, his/her mind is
  bright &amp; clear; and after giving is gratified. These are the three
  factors of the donor.
  
  "And which are the three factors of the recipients? There is the case
  where the recipients are free of passion or are practicing for the
  subduing of passion; free of aversion or practicing for the subduing
  of aversion; and free of delusion or practicing for the subduing of
  delusion. These are the three factors of the recipients.
  
  "Such are the three factors of the donor, the three factors of the
  recipients. And this is how a donation is endowed with six factors."


http://www.accesstoinsight.org/tipitaka/an/an06/an06.037.than.html

In brief, before giving have a joyous mind, have a mind that is bright and clear during the offering, and be pleased with the offering once you have made it. This is the best way to make offerings.