I'm looking for the differential gene expression in a somatic embryogenesis process. The thing is that i need to compare 5 conditions (stages) versus "control", each condition with two replicates. My question is... can i compare all in one run or do i need to compare by pares? And... how can i manage the replicates?

I started creating a count matrix (with data from the htseq count) comparing one condition versus control (with the 2 replicates of each one), and this command line: 

countsTable <- read.csv("controlvs9.csv", header=F, sep="\t")
colData = data.frame(condition = factor(c( "control", "control", "9days", "9days"))) 
dds <- DESeqDataSetFromMatrix(countData=countsTable, colData = colData, design=~condition))

and i get the results in 4 columns (because of the replicates", but i dont know if this is ok. i was expecting to get only two: control and 9days.

and also... i can't asign the first column which contains the names of the genes. 

hope someone can help me

You would use a design, ~condition, where that variable is a factor with the five stages and control as levels. Control should be the reference level (see vignette). Then you only need to run DESeq() once and you can compare levels with the results() function and the contrast argument. The replicates are handled automatically. The gene names will propagate as row names if you put them as row names on the counts.