Academic Affiliation - Paper will be Resubmitted during PhD but published as an AP in another institution I have a paper that needs to be resubmitted by the end of the week. It should be the last round, and I strongly expect the paper to be accepted for publication after that. 

I am still employed as a Ph.D. student in institution A, but will move to institution B as an assistant professor at the beginning of May. 

Thus, the paper will be published while I am working for institution B. Institution B provide financial incentives for such publication, and it would, therefore, be beneficial for me to put the affiliation "B" on the paper. 

What is the proper affiliation to put? I would tend to list both A and B as my affiliations, with a short footnote explanation.
Affiliation is primarily so that people can contact you and so that names can be disambiguated. On the other hand, you probably need to honor the institution that enabled your work. List an email and and affiliation that will be useful to people after publication. But in the acknowledgements you can indicate the prior affiliation with appropriate thanks. 

However, their are some scientific fields in which work is only possible in a lab funded by some entity that must be credited. In those fields, the PI is generally also listed as a co-author of the work, even if s/he does little of the actual research. In those fields it may be necessary, largely for political reasons, to use an affiliation under which the work was done. In such a case, it will be a bit of a dance to do something in the paper that helps readers find you if necessary. Or else you can arrange to have all attempted contacts forwarded to you in the future.