When (with reference to the era of the conquest of Eretz Yisrael), the Torah forbids doing all that we are doing ''today'' (in the Mishkan) it is drawing a distinction between the Korbanos that they had been bringing until then, and those that they would be bringing when they entered the Land (Rashi).
Interestingly, the Torah Temimah, based on the Gemara in Zevachim, interprets ''today'' as the post-Mishkan period, and what the Pasuk is therefore saying is that once the Mishkan is built, Yisrael will no longer be permitted to sacrifice on private Bamos (altars) as they will have been doing up until that time.
In any event, the Pasuk that follows indicates that there is a clear distinction between the period prior to and of the actual eras of the Mishkan and of the Beis-Hamikdash. The Torah Temimah explains the Pesukim and the ensuing Halachos in the following manner.
Following on from the earlier Pesukim which describe the obligation to build a house for G-d and bring our Korbanos, Ma'asros (i.e. Ma'aser-Sheini) and Bikurim there, the Pasuk here adds that once that is achieved, it will no longer be possible to bring Korbanos wherever one sees fit - to teach us that:
a. Bamos would become permitted after they entered Eretz Yisrael, and
b. they would be forbidden again once the Mishkan was built.
On the other hand, with reference to the period when Bamos were permitted, the Torah writes "every man whatever he sees fit", intimating that not all Korbanos may be brought on a Bamah, but only what may be brought voluntarily (i.e. Nedorim and Nedovos) that are eligible - not sin-offerings and other obligations. And this restriction in turn, is confined to private Korbanos. The Torah specifically writes "Ish", implying that although obligatory Korbanos Yochid may not be brought on a Bamah, obligatory Korbanos Tzibur may (Zevachim 117b).
Historically speaking, before the Mishkan was constructed in the second year in the desert, the people were permitted to build their own Bamos, on their rooftops or in their backyards, and so they did once again after they arrived in Gilgol, shortly after crossing the River Yarden and for the first fourteen years, during the conquest and distribution of the Land. And this concession applied, in spite of Moshe's Mishkan, which was still standing at that time. This was because the Din of Mishkan is linked (in Parshas Acharei-Mos) to the camp of Yisrael (i.e. the formation of Machaneh Yisrael in the desert), and during the era of Gilgol, the concept of Machaneh Yisrael was already obsolete.
With the death of Yehoshua, they rested from the conquest of the land, and moved the Mizbei'ach and the Aron of Moshe to Shiloh. Indeed, that is why the Torah refers here to Mishkan Shiloh as 'Menuchah', and that is when Bamos became forbidden once again. The concession to sacrifice on them returned after the destruction of Mishkan Shiloh in the days of Eli ha'Kohen (three hundred and sixty-nine years later), and it remained in force as long as the Aron was situated first in Nov and then in Giv'on, until Shlomo Hamelech built the Beis-Hamikdash, from which time Bamos became forbidden forever. This is clear from the fact that "el ha'Menuchah" hints to the concession of Bamos until the Mishkan is built, and "ve'el ha'Nachalah" (the Inheritance) to the concession of Bamos between the destruction of Shiloh and the Beis-Hamikdash, whereas there is no hint of any concession to build Bamos after that.
There were in fact, two kinds of Bamos, a Bomas Yochid and a Bomas Tzibur, such as the ones that existed in Nov and Giv'on. These are also known as 'Bamah Ketanah' and 'Bamah Gedolah' respectively. Building a Bamah Gedolah was forbidden whenever a Bamah Ketanah was forbidden. There were however, a number of differences between them, based mainly on the fact that the Shechinah rested on the Bamah Gedolah, which it did not on a Bamah Ketanah. Consequently, wherever the Torah writes "lifnei Hashem" (before G-d), the issue mentioned there pertains to a Bamah Gedolah, but not to a Bamah Ketanah. These include - 'Semichah' (leaning one's hand on one's Korban), the Shechting of Kodshei Kodshim in the north, the performing of the Avodah by a Kohen wearing the Bigdei Kehunah and using a 'K'li Shareis' (a sanctified vessel). All of these (among other things) did not apply to a Bamah Ketanah.
