Manually define clusters in Seurat and determine marker genes
I think you are looking to FindAllMarkers function from Seurat. As you said, you just have to define your ident, that have to have the structure of a table (cell names as names and cluster as value):

pident=as.factor(clusters)
names(pident)=cellNames    
object1@ident=pident


And then run the FindAllMarkers function:

FindAllMarkers(object1, min.pct = 0.25, min.diff.pct = 0.25)


You can specify several parameters in this function (type of DE to perform, thresholds of expression, etc).