The next part of the sonnet is a little bit trickier: "when feeling out of sight / For the ends of Being and ideal Grace" (3-4). This is an ambiguous passage, but we like to interpret this as the speaker "feeling for" the edges of her "Being" that are just "out of sight" – just the way that you try to feel for a glass of water on your bedside table that's just beyond your peripheral vision. As she's trying to feel the full extent of her soul, she realizes that she loves "thee" in every part of it – to the "depth and breadth and height" that it reaches.
To put it another way, when the speaker is trying to figure out ("feeling") how far her soul (her "Being") extends in the world, she realizes that her love for the beloved extends just as far (that's all the "depth and breadth and height" stuff in line 3).
Notice that if you put the "feeling" together with the "reach," this metaphor is very reliant on images of touch. We get the sense that the speaker is stretching out with both arms, trying to explain how broad and wide and deep her love is. It's a much more poetic version of saying "I love you THIS MUCH" with your arms flung wide.
Anyway, this spatial love is the first of the "ways" of loving that the speaker lists.