Anchors are your friend and should help you get your loops perfected, but there are some cautions. An anchor can be placed anywhere past the last anchor. I.e., Engine DJ will not let you place an anchor before the last one
Generally, you should place your anchor on the downbeat at the start of a measure. When you place an anchor the beat grid is shifted from the track beginning or the last anchor through the rest of the track. You can alter the grid from the last anchor forward by changing the BPM after it (or adding another anchor). The closest beat on the grid will snap to the anchor, so watch that the downbeat (first of measure) snaps there. If not, delete the anchor and change the BPM so the downbeat is close and reset it. Make sure your BPM is set correctly so the grid is matching the beats.
Work from the beginning to end of the track with your anchors and get your loops correct before moving onward. Although you may delete an anchor before the last one, you won’t be able to set another one before the last.
If you work with older tracks, such as classic disco, with variable BPM, it sometimes helps to load the track in Ableton Live, warp it with Complex Pro and export it back out. Warping may even out the BPM and make it easier to grid in Engine DJ. But, check carefully, warping can distort the music. While Ableton Live tries to force the beats to a set BPM (warping), Engine DJ lets you identify the beats with the grid, and doesn’t alter the true BPM.