Let $X$ be a quasi-projective variety, and let $L_1,...,L_n$ be ample line bundles on $X$. Is that true that if $E= \oplus L_i$, then
$$\mathbb{P}(E) \cong Proj(\bigoplus_{i_j \in \mathbb{N}^n} H^0(L_1^{\otimes i_1} \otimes...\otimes L_n^{\otimes i_n}))?$$
It is not true if $L_i$ are not ample, because then a priori $H^0(L_1^{\otimes i_1} \otimes...\otimes L_n^{\otimes i_n})$ may be 0 for any choice of $i_j$ (take for example on $\mathbb{P}^1$, $L_i=O(-i)$). I think that if $X$ is projective then it is true, maybe we could use that $H^0(O_X(1)) \otimes H^0(O_X(n)) \to H^0(O_X(n+1))$ is surjective for $n$ big enough, but I haven't been able to do it though.
I was so sure that this result was going to be false, and wrote something below saying to look at using relative proj instead. If that's what you were looking for, the original answer is at the bottom.
However, I think the claim is true if $X$ is projective, so, if you're interested, please check my work on this. If $X$ is quasi-projective, you have way too many sections, so there's no chance it'd work. For example, we could let $X=\mathbb{A}^1$ and $\mathscr{E}=\mathscr{O}$, in which case you're taking Proj of a ring that is not even finitely generated in degree 1.
First, we use the concept of an ample vector bundle, which was given in the answer here: How do we define ample vector bundles. One of the equivalent definitions of an ample vector bundle $\mathscr{E}$ over $X$ was that the tautological line bundle $\mathscr{O}_{\mathbb{P}\mathscr{E}}(1)$ is ample on $\mathbb{P}\mathscr{E}$.
So now there are two things to see:
1) The direct sum of ample vector bundles is ample.
2) $H^{0}(Sym^r\mathscr{E})=H^0(\mathscr{O}_{\mathbb{P}\mathscr{E}}(r))$.
It's probably possible to see this directly, but it's late, so I'm just going to dig through the article (http://archive.numdam.org/ARCHIVE/PMIHES/PMIHES_1966__29_/PMIHES_1966__29__63_0/PMIHES_1966__29__63_0.pdf ) given in the linked answer above to see that it's true. Claim 1) is given in Proposition 2.2, and this I think can be done directly from the definition.
Claim 2) is a special case of Lemma 3.1, where we let $F=\mathscr{O}_X$ to get $Sym^r\mathscr{E}=\pi_{*}\mathscr{O}_{\mathbb{P}\mathscr{E}}(r)$ where $\pi: \mathbb{P}\mathscr{E}\rightarrow X$ is the projection.
Finally, putting the two together, we get that $\mathscr{O}_{\mathbb{P}\mathscr{E}}(1)$ is ample, so $\mathbb{P}\mathscr{E}=Proj(\oplus_{r\geq 0}{H^0(\mathscr{O}_{\mathbb{P}\mathscr{E}}}(r)))=Proj(\oplus_{r\geq 0}{H^{0}(Sym^r\mathscr{E})})$, which is equal to the formula you gave above in the case where $\mathscr{E}$ is a direct sum of ample line bundles.
Original answer:
It seems to me that what you're looking for is the relative proj construction. In the relative proj construction, instead of having a graded ring over some base ring $A$, we have a sheaf of graded algebras over a scheme $X$. Over each open affine ${\rm Spec}(A)$ in $X$, the relative proj agrees with the usual version, and it glues together to a projective scheme over $X$.
Given that, if we have a locally free sheaf $\mathscr{F}$, we have $\mathbb{P}\mathscr{F}=\mathcal{Proj}({\rm Sym}^{\cdot}\mathscr{F})$ (whether we take the dual $\mathscr{F}^{\vee}$ inside of the symmetric power depends on your convention for what $\mathbb{P}\mathscr{F}$ means). If you assume $\mathscr{F}$ splits as a direct sum of line bundles and expand, you get something similar to your formula, but as a sheaf of graded rings over $X$ instead of just one graded ring. For a reference, this is definition 17.2.3 in Vakil's notes (http://math.stanford.edu/~vakil/216blog/FOAGdec2915public.pdf).