How much do editors care about author affiliations and previous publications in the field? we've wrote a manuscript applying a computational modelling technique to a field (behavioral ecology) which is not related to our primary research field (neurobiology). This was the result of some year and a half of work, as a parallel project that we took interest upon.

The thing is, the institute to which we're affiliated has nothing to do with the theme of the manuscript, nor we have any published experience in said field.

How much will that matter for acceptance? Do editors take affiliations into consideration? Does it matter which journal (say, Nature cares but PLoS Computational Biology doesn't)?

Thanks.
In principle your background and affiliation should play no role, and the manuscript will be handled and reviewed on its merits only. Now, in practice, editors are only human, and may subconciously show some bias against unknown authors, and may deal with the paper with more skepticism than usual. However I do believe that most editors are professional enough to give the manuscript a fair evaluation.

Of course the very top journals are very selective, so that even for well-known authors in the field it is difficult to get published there. Especially if you are new to a field, it might be a good idea to first get feedback on your manuscript from someone who is more familiar with the field, to avoid disappointment.