Usually ectopic integration of DNA into the fungal genome is preferred because most filamentous fungi employ a powerful repair system for non-homologous end-joining (NHEJ). On the other hand, homologous recombination occurs when your sequence of interest is flanked by genomic regions of the fungus you transform. The minimum length can vary greatly among different species. In the latter case (i. e. when two recombination events take place) the plasmid is not integrated into the genome and subsequently lost due to lack of selection.

Cheers, Christian 

Thank you very, that what I want to know 

Dear Lucia, transformations using deletion cassette flanked by 300-400 bp homologous regions for the deletions in Hansenula polymorpha work very efficiently. From where did you get the information regarding to 800-1000 bp? 

you need to do homologous DNA integration if you are knocking out, otherwise ectopic integration will be a good choice.