Just subtract a number:
> as.Date("2009-10-01")
[1] "2009-10-01"
> as.Date("2009-10-01")-5
[1] "2009-09-26"
Since the Date class only has days, you can just do basic arithmetic on it.
If you want to use POSIXlt for some reason, then you can use it's slots:
> a <- as.POSIXlt("2009-10-04")
> names(unclass(as.POSIXlt("2009-10-04")))
[1] "sec" "min" "hour" "mday" "mon" "year" "wday" "yday" "isdst"
> a$mday <- a$mday - 6
> a
[1] "2009-09-28 EDT"