### Solution:

#### Part (1): Proving the sequence $\{a_{n+1}-2a_{n}\}$ is an arithmetic sequence

Given $S_{n+2}+3S_{n}=4S_{n+1}-2a_{n}$, and initial values $a_{1}=1$, $a_{2}=3$, we proceed as follows:

1. We start by expressing $S_{n+2}-S_{n+1}$ in terms of $S_{n+1}-S_{n}$ and $a_{n}$:
$$S_{n+2}-S_{n+1}=3(S_{n+1}-S_{n})-2a_{n}$$
This equation essentially gives us the difference between consecutive terms of the sequence in terms of the previous terms.

2. Since $S_{n+2}-S_{n+1}=a_{n+2}$ and $S_{n+1}-S_{n}=a_{n+1}$, we can rewrite the equation as:
$$a_{n+2}=3a_{n+1}-2a_{n}$$
This gives us a recursive formula for the sequence.

3. To prove $\{a_{n+1}-2a_{n}\}$ is an arithmetic sequence, we examine the difference between consecutive terms:
$$(a_{n+2}-2a_{n+1})-(a_{n+1}-2a_{n})=0$$
This shows that the difference between consecutive terms of $\{a_{n+1}-2a_{n}\}$ is constant, hence it is an arithmetic sequence.

$\boxed{\text{The sequence } \{a_{n+1}-2a_{n}\} \text{ is an arithmetic sequence.}}$

#### Part (2): Finding $T_{n}$, the sum of the first $n$ terms of the sequence $\{b_{n}\}$

1. From part (1), we know $a_{n+1}-2a_{n}=1$, leading to $a_{n+1}=2a_{n}+1$.

2. This recursive formula can be solved to find $a_{n}$:
$$a_{n+1}+1=2(a_{n}+1) \Rightarrow a_{n}+1=2^{n}$$
This gives us an explicit formula for $a_{n}$ in terms of $n$.

3. Substituting $a_{n}+1=2^{n}$ into the given formula for $b_{n}$:
$$b_{n}=\frac{n+2}{(n^{2}+n)2^{n}}=2\left[\frac{1}{n2^{n}}-\frac{1}{(n+1)2^{n+1}}\right]$$
This simplification reveals $b_{n}$ as a telescoping series.

4. The sum $T_{n}$ can then be found by summing the series:
$$T_{n}=2\left[\frac{1}{1\cdot2^{1}}-\frac{1}{2\cdot2^{2}}+\cdots+\frac{1}{n\cdot2^{n}}-\frac{1}{(n+1)\cdot2^{n+1}}\right]=1-\frac{1}{(n+1)\cdot2^{n}}$$
This final step utilizes the telescoping nature of the series, where most terms cancel out, leaving only the first and the last.

$\boxed{T_{n}=1-\frac{1}{(n+1)\cdot2^{n}}}$