Pricing from Taxstra to me sounds reasonable for what they are offering for filing your personal return with multiple schedule E's for the investments.

• Timeline & Scheduling: • How long will the project take?

This means that when you sell the property, your adjusted tax basis is lower, which increases the capital gain you must recognize.Additionally, any accelerated depreciation taken is subject to depreciation recapture at a higher tax rate (up to 25% for real estate assets) rather than being taxed as long-term capital gains.So, while cost segregation provides significant upfront tax savings, it also increases your capital gains tax liability upon sale unless you use a 1031 exchange or other tax-deferral strategies.You can find your current tax basis by reviewing your depreciation schedule (Form 4562) and prior years’ tax returns, specifically looking at your adjusted basis on Form 4797 (for sales of business property) or Schedule D (for capital gains and losses).Your CPA should be consulted prior to making any decisions. 

I would make the expense codes mimic the Schedule E if using quickbooks.

It all still goes on Schedule E. 

But since you have already taken bonus depreciation while it was an LTR, this may not even be a concern for you.There're other potential complications such as a different depreciation schedule, treatment of previously suspended losses, and so on.

What some companies do and maybe something you should try is setting up a split payment schedule for them but for a fee and make a little extra scratch. - if you do this make sure it is well documented so that your eviction will not skip a beat if something goes wrong. 

Can I use both as an expense when filling out my schedule E?

Can you deduct on Schedule E, or can it only be used on Schedule C?

Reach out or schedule a call if you have any direct questions, I'l be happy to answer them all!