It is not clear what you are doing wrong as you don't provide a reproducible example of the problem and I am having difficulty following your description of what is wrong. Here is a fully worked out example for you to follow that does what you seem to being trying to do.
data(varespec)
data(varechem)
ord <- rda(varespec)
set.seed(1)
(fit <- envfit(ord, varechem, perm = 999))
## make up a fake `status`
status <- factor(rep(c("Class1","Class2"), times = nrow(varespec) / 2))
> head(status)
[1] Class1 Class2 Class1 Class2 Class1 Class2
Now plot
layout(matrix(1:2, ncol = 2))
## auto version
plot(fit, add = FALSE)
## manual version with extra things
colvec <- c("red","green")
scl <- -1
plot(ord, type = "n", scaling = scl)
points(ord, display = "sites", col = colvec[status], pch = (1:2)[status])
points(ord, display = "species", pch = "+")
plot(fit, add = TRUE, col = "black")
layout(1)
Which gives
And all the arrows seem to be pointing as they would if you plotted the envfit
object directly.