thank you for your answer
I understand that it's ok to use different methods for binary and normal traits. the results for normal traits look the same with both methods.
out.sc1<-scanone(mycross, pheno.col=c(1:11), method="hk", model="normal")
out.sc1.bin<-scanone(mycross, pheno.col=c(12:13), method="em", model="binary")
for the addqtl I have to use perms of the scanone results?